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© © All Rights Reserved
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Chemistry
for the Life Sciences
Second Edition
Chemistry
for the Life Sciences
Second Edition

Raul Sutton, Bernard Rockett, and Peter G. Swindells


CRC Press
Taylor & Francis Group
6000 Broken Sound Parkway NW, Suite 300
Boca Raton, FL 33487-2742
© 2009 by Taylor & Francis Group, LLC
CRC Press is an imprint of Taylor & Francis Group, an Informa business

No claim to original U.S. Government works


Version Date: 20110715

International Standard Book Number-13: 978-1-4200-6936-5 (eBook - PDF)

This book contains information obtained from authentic and highly regarded sources. Reasonable efforts have been
made to publish reliable data and information, but the author and publisher cannot assume responsibility for the valid-
ity of all materials or the consequences of their use. The authors and publishers have attempted to trace the copyright
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Contents

Preface xi

1 Elements, Atoms, and Electrons 1


1.1 Introduction 1
1.2 Matter and Elements 1
1.3 Atoms 1
1.4 Atomic Structure 2
1.5 Isotopes 5
1.6 The Periodic Table 6
1.7 Electron Structure of Atoms 7
Summary 13
Suggested Further Reading 13
End-of-Chapter Questions 13

2 Covalent Bonding and Molecules 15


2.1 Introduction 15
2.2 Interactions between Atoms 15
2.3 Covalent Bonds Are Formed by Sharing Outer Electrons 15
2.4 Formulae of Compounds 19
2.5 Covalent Bonds Formed by Combining Atomic Orbitals 23
2.6 Single Overlap, the Sigma-Bond 24
2.7 Double Overlap, the Pi-Bond 25
2.8 Molecules with σ- and π-Bonds 27
2.9 Hybrid Molecular Orbitals 28
Summary 30
End-of-Chapter Questions 31

3 Forces Within and Between Molecules 33


3.1 Introduction 33
3.2 Ionic Bonding 33
3.3 Polar Covalent Bonds 35
3.4 Dipole–Dipole Forces 37
3.5 The Hydrogen Bond 38
3.6 van der Waals Forces 40
3.7 The Hydrophobic Effect 41
3.8 Coordinate Bonds 42
Summary 43
End-of-Chapter Questions 43

4 Chemical Reactions 45
4.1 Introduction 45
4.2 Rates of Reaction 45


4.3 Factors Affecting Rate of Reaction 45
4.4 Rate Equations 46
4.5 Integrated Forms of Rate Equations 46
4.6 Zero-Order Reactions 46
4.7 Integrated Form of the Zero-Order Rate Equation 47
4.8 First-Order Reactions 47
4.9 The Integrated Form of the First-Order Rate Equation 47
4.10 Second-Order Reactions 48
4.10.1 Type 1 48
4.10.2 Type 2 48
4.11 Integrated Forms of Second-Order Rate Equations 48
4.11.1 Type 1 48
4.11.2 Type 2 49
4.12 Pseudo-First-Order Reactions 49
4.13 Reversible Reactions 50
4.14 Equilibrium 51
Summary 53
Suggested Further Reading 54
End-of-Chapter Questions 54

5 Water 55
5.1 Introduction 55
5.2 The Water Molecule 55
5.3 Ice 55
5.4 Water 55
5.5 Solutions 56
5.6 The Mole Concept 57
5.7 Calculating Molar Masses 57
5.8 Molarity 58
5.9 Colloidal Solutions 59
5.10 Diffusion and Osmosis 60
Summary 61
Suggested Further Reading 61
End-of-Chapter Questions 61

6 Acids, Bases, and Buffers 63


6.1 Introduction 63
6.2 Ionisation of Water 63
6.3 The Hydrogen Ion 63
6.4 Acids and Bases 64
6.5 Strong Acids and Strong Bases 64
6.6 Weak Acids and Weak Bases 64
6.7 Ka and Kb 65
6.8 Relationship between Ka and Kb 66
6.9 pH, pOH, pKw, pKa, pKb 66
6.10 Solutions of Weak Acids and Bases 68
6.11 Salts and Salt Hydrolysis 70
6.12 Buffer Systems 71
6.13 Calculating the pH Values of Buffers 72
6.14 Indicators 75
6.15 Titrations 75

vi Chemistry for Life Sciences


Summary 77
Suggested Further Reading 77
End-of-Chapter Questions 77

7 Gases 79
7.1 Introduction 79
7.2 Pressure 79
7.3 Measurement of Pressure 79
7.4 Ideal Gas Laws 82
7.5 Partial Pressures 85
7.6 Solubility of Gases 87
7.7 Diffusion in Gases 88
Summary 89
Suggested Further Reading 90
End-of-Chapter Questions 90

8 Aliphatic Carbon Compounds 91


8.1 Introduction 91
8.2 Simple Molecules Containing Carbon 91
8.3 Organic Compounds 93
8.4 Alkanes and Alkyl Groups 93
8.5 Alkenes 97
8.6 Alcohols 98
8.7 Thiols 100
8.8 Aldehydes and Ketones 101
8.9 Carboxylic Acids 103
8.10 Amines 106
Summary 108
End-of-Chapter Questions 109

9 Lipids, Sugars, and Linkages between Reactive Groups 111


9.1 Introduction 111
9.2 Fatty Acids 111
9.3 Esters 114
9.4 Glycerol Esters 115
9.5 Hemiacetals and Hemiketals 116
9.6 Simple Sugars 117
9.7 Chirality in Simple Sugars 119
9.8 Straight-Chain Sugars Spontaneously Form Rings 121
9.9 Sugar Hydroxyls Can Be Chemically Modified 122
9.10 Sugars Are Joined Together by Glycosidic Bonds 122
Summary 124
Suggested Further Reading 124
End-of-Chapter Questions 125

10 Aromatic Carbon Compounds and Isomerism 127


10.1 Introduction 127
10.2 Benzene 127
10.3 Bioactive Aromatic Compounds 130
10.4 Isomerism 134
10.5 Structural Isomerism 134

Contents vii
10.6 Chain, Positional, and Functional Group Isomerism 134
10.7 Tautomerism 138
10.8 Stereoisomerism 138
10.9 Geometrical Isomerism 139
10.10 Optical Isomerism 140
Summary 143
End-of-Chapter Questions 143
11 Organic and Biological Reaction Mechanisms 147
11.1 Introduction 147
11.2 Reactive Sites and Functional Groups 147
11.3 Describing Reaction Mechanisms    150
11.4 Bimolecular Nucleophilic Substitution 151
11.5 Electrophilic Addition to a Nonpolar Double Bond 152
11.6 Elimination to Form an Alkene 153
11.7 Nucleophilic Addition to a Polar Double Bond 157
11.8 Free Radical Reactions 159
11.9 Carbon–Carbon Bond Formation in Biosynthesis 161
Summary 163
Suggested Further Reading 164
End-of-Chapter Questions 164
12 Sulphur and Phosphorus 165
12.1 Introduction 165
12.2 The Electron-Shell Structure and Valency of
Phosphorus and Sulphur 165
12.3 Sulphur 167
12.4 The Thiol Group and Thiol Esters 170
12.5 Phosphate, Pyrophosphate, and Polyphosphate 172
12.6 Phosphate Esters 173
12.7 The Role of Phosphate Esters and ATP in
Cellular Energy Metabolism 175
Summary 177
Suggested Further Reading 177
End-of-Chapter Questions 177
13 Oxidation and Reduction Reactions 179
13.1 Introduction 179
13.2 Oxidation Is Linked to Reduction 179
13.3 The Chemical Changes in the REDOX Process 180
13.4 Splitting REDOX Reactions 180
13.5 Standardising REDOX Half-Reactions 182
13.6 Predicting Electron Flow 183
13.7 Free Energy and Standard Reduction Potentials 184
13.8 Redox Reactions and Nonstandard Conditions 185
Summary 187
Suggested Further Reading 187
End-of-Chapter Questions 187
14 Metals in Biology 189
14.1 Introduction 189
14.2 General Properties of Metals in Biology 189

viii Chemistry for Life Sciences


14.3 Some Properties of Alkali Metals 192
14.4 The Alkaline Earth Metals 193
14.5 Transition Metals 194
14.6 Role of Metal as Oxygen Carrier 194
14.7 Metals Facilitate Biocatalysis 195
14.8 The Role of Metal Ions as Charge Carriers 196
14.9 The Toxicity of Metals 198
Summary 199
Suggested Further Reading 199
End-of-Chapter Questions 200

15 Energy 201
15.1 Introduction 201
15.2 The First Law of Thermodynamics 201
15.3 Units of Energy 202
15.4 Measurement of Energy 202
15.5 Internal Energy, U, and Enthalpy, H 202
15.6 Calorimetry 203
15.7 Hess’s Law 204
15.8 Enthalpies of Formation 206
15.9 The Second Law of Thermodynamics 208
15.10 Free Energy 209
15.11 Interaction of ∆H with T∆S 209
Summary 211
Suggested Further Reading 211
End-of-Chapter Questions 211

16 Reactions and Equilibrium 213


16.1 Introduction 213
16.2 ∆G and Equilibrium 213
16.3 Activation Energy 215
16.4 The Effect of the Temperature on Reaction Rate 216
16.5 The Arrhenius Equation 217
16.6 Catalysis 218
16.7 Enzyme Catalysis 219
16.8 Kinetics of Enzyme Reactions 220
16.9 Finding Vmax and K M 221
Summary 223
Suggested Further Reading 223
End-of-Chapter Questions 223

17 Light 225
17.1 Introduction 225
17.2 Light Is Part of the Electromagnetic Spectrum 225
17.3 Wavelength and Frequency 225
17.4 The Quantum Theory of Light 227
17.5 The Absorption of Light 229
17.6 The Relationship between Light Absorption and
Concentration 231
17.7 The Spectrophotometer 233
17.8 The Fate of Absorbed Light 234

Contents ix
Summary 236
Suggested Further Reading 236
End-of-Chapter Questions 236

Appendix: Derivations of Equations 239

Index 249

 Chemistry for Life Sciences


Preface

Introduction and Use of This Text

This book is intended as a self-study text for first-year undergraduate life


scientists. As such a student, you will be expected to study some bio-
chemistry during your course and will need understanding of selected
fundamental chemical concepts in order to underpin this teaching. Thus,
we aimed to include only those aspects of chemistry that would be rel-
evant to you, the life scientist. So, each chapter begins with an introduc-
tion that explains the biological relevance of the contents. We have made
a conscious effort to eliminate the overlap with conventional biochemis-
try textbooks. The relevance of the material to you is given importance
by the choice of biologically relevant examples, ­wherever possible. The
text expects little in the way of prior knowledge of ­chemistry and intro-
duces concepts at a basic level. However, the depth that the text seeks to
achieve means that many concepts are introduced and expanded within
a short space. This keeps each ­ chapter brief while covering most of
the necessary material that you will require during your undergraduate
course. The text provides you with a concise introduction to chemistry.
Many undergraduate life scientists have not studied mathematics
beyond the General Certificate of Secondary Education (GCSE), and
we have assumed little prior knowledge of mathematics when writing­
this text. Chemistry relies, in part, on physical principles, many of
which are derived from fundamental considerations of equilibrium
thermo­dynamics. The origin of equilibrium thermodynamics requires a
reasonable grasp of algebra and calculus. We have removed such deriva-
tions from the text and presented only the equations that you will use
when performing calculations. You may wish to satisfy your natural
curiosity, and so the derivations and origins of important equations are
included in an appendix.
We realise that you may not feel confident in tackling problems of
which you have had little prior experience. Each chapter helps you
in areas involving calculations by illustrating each important type of
­calculation with step-by-step worked examples. You can then test your
understanding of the steps involved by attempting the questions pro-
vided in the text. These in-text questions are supported by a set of fully
worked answers that are available from the publisher so that you can
check your approach to problem solving.
Some of the material covered in the chapters will require rote learn-
ing, and this is something that you will have to work toward. It would
not be practical for you to remember all such names at the first attempt.
Rote learning can be made easier by breaking down the material into

xi
small parts. The regular review of such material will also aid your
memory. It is similar with other ideas that are introduced in the text.
Physical concepts can sometimes seem daunting to the life scientist, but
rereading material that you find difficult, slowly and carefully, will help
you to gain a much clearer understanding of its meaning. In all areas of
the book, there are worked examples of answers to questions that help
you to learn and in-text questions to help you reassure yourself that you
understand the part of the book that you are reading.
We use the term “biomolecule” freely throughout the text to denote a
molecule that is an important constituent of living organisms. Many of
the chemical reactions undertaken by living organisms take place in a
controlled environment, often at or near pH 7.0. Consequently, pH 7.0 and
25°C are assumed to be standard conditions for the purposes of this text.
The chemistry that you learn here will be used in many areas of your
future study in subjects such as physiology, pharmacology, microbiology,
and biochemistry. A deeper understanding of biology can come only
when the structure, reactivity, and physical processes of the molecules
that make up the varied living world around us are understood. This
book will help you to appreciate this important area of the life sciences.

The Second Edition

We thought carefully about the structure of the first edition and in this
text have made several improvements. One of the major improvements
is the introduction of important chemical concepts that cover aspects
of life sciences chemistry. Thus, the new edition includes amended and
extra topics in the following subject areas:
• A separate chapter on the behaviour and properties of water
• Structure, behaviour, and reactivity of aromatic molecules
• Metals in biological organisms
• Gases, diffusion, and osmosis
We have removed the answers to self-assessment questions from the text
and placed these in a Solutions Manual available through the ­publisher.
This keeps the text concise, and the price competitive, while still ­making
the worked answers to questions available to you.
We are also conscious that the material presented in this text may
be used to support the creation of a lecture series in relevant areas of
first-year chemistry teaching. Thus, many of the tables and figures used
in the text are available on the publisher’s Web site in downloadable
format. This will enable you to integrate the text into your lecture series
to create a consistent whole for the chemistry that you teach.
In addition, we recognise that the nature of chemistry changes as
does the impact of such chemistry on our understanding of biology.
Advances in biology mean that there may be changes to the focus of
a text such as this. We have, after careful research, covered the most
important topics of chemistry relevant to the life scientist. However,
we welcome feedback on the text, in order to keep abreast of necessary
changes in subject focus in the future.

xii Chemistry for Life Sciences


Finally, we wish to thank Dr. John Edlin for permission to reproduce
the periodic table used in Chapter 1.

Raul Sutton
Bernard Rockett
Peter Swindells

Preface xiii
Elements, Atoms, 1
and Electrons
1.1 Introduction

In order to understand the nature and reactions of biological molecules


that often have large or complex structures, it is helpful to examine the
simplest units of matter first. This topic will show how a few elemen-
tary particles, protons, neutrons, and electrons, can be used to build the
atoms of elements and how the electrons are organised within atoms.
This organisation determines the properties of the atom and how ele-
ments will combine within a living organism.

1.2 Matter and Elements

Picture on the one hand the darting flight of an iridescent dragonfly


and on the other hand a pile of soil. The first is brilliant, dynamic, and
organised; the second is dull, featureless, and inert. It does not seem
possible that the two can be related in any way, but we know that each
is composed of the simple substances called elements. The 92 naturally
occurring elements combine in a variety of ways to make up all the
organisms and materials of the world we live in.
An element is a single substance that cannot be split by chemical
means into anything simpler. Carbon is the building block of life; it is Each element is a single, simple
an element and cannot be split into anything simpler. Of the large substance; it cannot be split by
chemical means.
number of natural elements, only a few are of importance in the living
world. Some assume major significance as macronutrients, and others
are required in small quantities as trace elements; these are shown in
Table 1.1 and Table 1.2.
In order to write biological substances in as clear and accurate a form
as possible, the different elements or atoms can be represented in a brief,
simple form called a symbol. Each element has a single capital letter as A symbol is used as a shorthand
the symbol; thus, carbon is represented as C and hydrogen as H. When form for an element.
more than one element begins with the same letter, then the symbol may
have a second, small letter added to it in order to avoid confusion. In this
way, calcium is shown as Ca, and chlorine is Cl. The conventional way
of writing a symbol should always be used; chlorine cannot be written
as CL or as cl. Symbols for biologically important elements are listed in
Table 1.1 and Table 1.2. An extended list is given in Table 1.5.

1.3 Atoms

Each element is made up of a large number of tiny but identical particles


called atoms. Thus, the element carbon is composed entirely of carbon
atoms; oxygen consists only of oxygen atoms. An atom is described as


Table 1.1 Elements of Major Importance to Plants and Animals
Element Name Symbol Role in Living Organisms Source Used by Man
Carbon C Constituent of protein, carbohydrate, fat Meat, fruit, vegetables
Hydrogen H Body fluid, essential for protein, carbohydrate, fat Water
Oxygen O Essential for respiration, body fluid, protein, Air and water
carbohydrate, fat
Nitrogen N Constituent of proteins, nucleic acids, Meat and fish
chlorophyll
Phosphorus P Essential for ATP, phospholipids, nucleic acids Meat and milk
Sulphur S Component of proteins, coenzyme A Meat, fish, eggs
Chlorine Cl Ion balance across membranes, stomach acid Table salt, salted
foods
Sodium Na Ion balance across membranes Table salt, salted
foods
Potassium K Anion–cation balance across membranes, Meat, green
nerve impulses vegetables
Calcium Ca Component of bones, teeth, invertebrate shells, Hard water, milk
plant cell walls, essential for blood clotting

the smallest particle into which an element can be divided while still
retaining the properties of the element. The very small size of a ­carbon
atom can be appreciated when it is found that 12 g of carbon contains
6 × 1023 individual atoms; this value is the Avogadro number. It is
important to us because it enables the masses of different elements to be
compared. One atom is much too small to be weighed easily, so we take
the mass of 6 × 1023 atoms of an element and call this the atomic mass
of the element. Thus, the atomic mass of carbon is 12 g. It is convenient
to compare the atomic mass of an element to one-twelfth of the atomic
mass of carbon and call the value obtained the relative atomic mass
(Ar). The relative atomic mass of carbon is 12 (there are no units), the
value for hydrogen is 1, and the value for oxygen is 16.

1.4 Atomic Structure

Even though an atom is the smallest chemically distinct particle of an


element, it does consist of smaller units, the subatomic particles. There
An atom consists of a nucleus are three types of subatomic particles found in atoms: protons, ­neutrons,
made up of protons and and electrons. The number and arrangement of these particles in the
neutrons, which is surrounded
by electrons. atom determine which element it is and how it will react in biological
or chemical processes. Each proton carries the same positive electrical
charge, and the neutron is electrically neutral. These two particles have
almost the same mass and are joined tightly together in the tiny central
part of the atom, the nucleus. Each electron carries a negative electrical
charge that exactly balances the positive charge on the proton. Electrons
have a very small mass compared with protons and neutrons. They are

 Chemistry for Life Sciences


Table 1.2 Trace Elements of Importance to Animals and Plants
Element Name Symbol Role in Living Organisms Source Used by Man
Boron B Healthy cell division in the growing points
of plants
Fluorine F Constituent of teeth and bones Hard water, milk
Iodine I Essential for thyroxine in thyroid Drinking water, sea food,
iodised table salt
Selenium Se Removal of active oxygen species by Fruit and vegetables
glutathione peroxidase
Manganese Mn Growth of bone Present in a range of foods
Iron Fe Oxygen carrier in myoglobin and Liver, red meat, spinach
haemoglobin, cofactor in many reduction/
oxidation (redox) reactions
Cobalt Co Essential for vitamin B12 promoting red Liver, red meat
cell development
Copper Cu Oxygen carrier in haemocyanin for certain Present in a range of foods
invertebrates; component of cytochrome
oxidase, an enzyme found in the
respiratory chain of almost all eukaryotes
Zinc Zn Essential in carbonic anhydrase for carbon Present in a range of foods
dioxide transport in blood
Molybdenum Mo Plant enzymes involved with nitrogen
fixation and formation of amino acids
Silicon Si Cell walls in plants, exoskeletons of
marine invertebrates

distributed around the nucleus in discrete energy levels or orbitals. The An electron in an atom is in
three subatomic particles are compared in Table 1.3. The same three rapid, random motion.
subatomic particles are present in the atoms of every element but occur
in different numbers and proportions in different elements.
The number of protons in the nucleus determines to which element the
atom corresponds. For example, hydrogen always has one proton in each
of its atoms, carbon has six protons, and oxygen has eight protons. This
number of protons in the nucleus of an atom of a given element is called
the atomic number or proton number. An atom is electrically neutral, The number of protons in the
which means that the number of protons and electrons must be equal. atom of an element is the atomic
number of the element.
Hydrogen has one proton and so has one electron, nitrogen has seven
protons and therefore must have seven electrons. The atomic nuclei of the
lighter elements often contain an equal number of ­neutrons and protons;

Table 1.3 Subatomic Particles


Approximate Relative
Particle Name Relative Mass Electrical Charge
Proton 1.0 1+
Neutron 1.0 0
Electron 0.002 1–

Elements, Atoms, and Electrons 


Table 1.4 Atomic Structure and Electron Structure of Isotopes of Biologically Important
Elements
Number of Protons Number of Number of
Element Name Symbol (Atomic Number) Neutrons Electrons Full Symbol
Hydrogen H 1 0 1 1H
1
Deuterium H 1 1 1 1H
2

Boron B 5 6 5 11 B
5
Carbon C 6 6 6 12 C
6
Carbon C 6 7 6 13 C
6
Carbon C 6 8 6 14 C
6
Nitrogen N 7 7 7 14 N
7
Oxygen 0 8 8 8 16 O
8
Sodium Na 11 12 11 11 Na
23

Magnesium Mg 12 12 12 12 Mg
24

Phosphorus P 15 16 15 31 P
15
Sulphur S 16 16 16 32 S
16
Chlorine Cl 17 18 17 35 Cl
17
Chlorine Cl 17 20 17 37 Cl
17

carbon has six protons and six neutrons, and oxygen has eight protons
and eight neutrons. Heavier elements tend to have a greater number of
neutrons than protons (see Table 1.5), but hydrogen is unique in having
no neutrons in the nucleus. The elements of biological importance are
shown in Table 1.4 with the numbers of subatomic particles in the atom.
The number of protons and neutrons in the atom and by implication,
the number of electrons, may be represented in a shorthand form based
on the symbol for the elements. The number of protons is shown below
(subscript) and to the left of the symbol—this is the atomic number.
The mass number is the sum
of the number of protons and The sum of the number of protons and neutrons is shown above (super-
neutrons in the element. script) and to the left of the symbol—this is the mass.

Worked Example 1.1


The element nitrogen, which is important in amino acids, has
seven protons and seven neutrons in the nucleus of the atom.
(i) Show this in terms of the element symbol.
(ii) How many electrons are there in the atom?

Answer

(i) Write the symbol for nitrogen N


Add the number of protons (7) below and to the left
of the symbol 7 N
Add the sum of the protons (7) and neutrons (7) above
and to the left of the symbol 14
7 N

 Chemistry for Life Sciences


(ii) The nitrogen atom has seven protons. The number of ­protons
equals the number of electrons in any atom, and thus, the
nitrogen atom has seven electrons.
When the symbol is provided, it can be used to find the number of
neutrons and electrons.

Worked Example 1.2


Boron is a trace element that promotes healthy cell division in
plants. It has the symbol 115 B. How many neutrons and how many
electrons are present in the atom?

Answer
The number of neutrons is obtained by subtracting the atomic
number (5) from the mass number (11):
11 – 5 = 6 neutrons
The number of electrons is five. This is because the number of elec-
trons is the same as the number of protons (the atomic number).

Question 1.1
Sodium is an element involved in the ionic balance across
membranes.
(i) How many electrons and neutrons are present in the atom?
(ii) Use Table 1.4 to write the symbol for the element to show the
mass number and atomic number.

1.5 Isotopes

It has been shown that the atom of a specific element contains a fixed
number of protons and electrons (for example, hydrogen always has one
proton and one electron; carbon invariably contains six protons and six
electrons, and so forth). However, the number of neutrons in the atom of
an element can vary.
Thus, a small proportion of hydrogen atoms have one neutron rather
than none and some carbon atoms have seven or eight neutrons, rather
than the more common six neutrons. These different forms of the same
element are called isotopes. They show the same chemical properties Different isotopes of an element
but have different mass numbers and thus different masses. have different mass numbers.

In the living organism, isotopes of an element are completely inter-


changeable with one another, though the heavier isotope reacts more
slowly. The difference in speed (rate) of reaction between the two forms
depends on the mass difference. Normal hydrogen (1H) has only half
the mass of deuterium (2H) and so it reacts considerably faster. The

Elements, Atoms, and Electrons 


symbol D often replaces 2H. Biochemical pathways are investigated by
­replacing hydrogen with deuterium, perhaps by substituting ­deuterium
oxide (heavy water D2O) for ordinary water (H2O). The fate of the
­deuterium in the pathway can be traced by routine analysis; hence, the
term “tracer” is often used for isotopes such as deuterium.
Isotopes of an element may be stable or unstable. Stable isotopes
such as 126 C and 136 C do not undergo any change in the atomic nucleus
with time, but unstable isotopes such as 146 C spontaneously decompose
at a fixed rate. It is the atomic nucleus of the isotope that decays. Such
behaviour is often associated with a high proportion of neutrons to
protons­ in the nucleus. A neutron in the nucleus of an unstable isotope
can break down to form a proton and an electron. The proton remains
in the nucleus while the electron is emitted at high energy and can be
detected with a suitable instrument. The high-energy electron is called
a β-particle­, and this type of breakdown is known as β-decay.
Conversion of a neutron in 146 C to a proton and an electron leaves the
nucleus with seven neutrons and seven protons; it becomes an isotope of
nitrogen. The reaction can be represented by an equation:
14
6 C → 147 N + β-particle
It takes place quite slowly, with half of the original amount of carbon-14
breaking down over a period of 5760 years. The decay of unstable
isotopes is known generally as radioactive decay. Radioactive decay
does not always result in the emission of β-particles. Some isotopes
emit α-particles (the nuclei of helium atoms, 42 He), and others emit
high-energy electromagnetic radiation (γ-rays) on decay.

Question 1.2
Write an equation to represent the β-decay of the radioactive
35 S.
­isotope 16

1.6 The Periodic Table

It is convenient to arrange the elements in order of increasing atomic


number. When this is done, it is found that the properties of the eight
light elements, lithium to neon, are repeated in the next eight elements,
sodium to argon. A table arranged to align in vertical columns elements
with similar properties is called a Periodic Table (Table 1.5).
Only a few of the elements are of significance in the life sciences, and
these are highlighted in Table 1.5. They are grouped mainly to the left
(metals) and to the right (non-metals) with a third group in the ­middle
(transition metals). The periodic table shows a number of trends, some
Electronegative atoms strongly of which are important in biological chemistry. Electronegativity,
attract electrons. which is the power of an element to attract electrons to its atoms, varies
in the periodic table. It increases on moving from left to right and from
bottom to top. Thus, the important biosphere elements nitrogen, oxygen,

 Chemistry for Life Sciences


Table 1.5 Periodic Table of the Natural Elements
1
1H
4
1.01 2 He
4.00
7 9 11 12 14 16 19 20
3
Li 4
Be 5B 6C 7N 8O 9F 10 Ne
6.94 9.01 10.8 12.0 14.0 16.0 19.0 20.2
23
13
Na 24
12
Mg 27
13 Al
28
14 Si
31
15 P
32
16 S
35
17 Cl
40
18 Ar
24.3 24.3 27.0 28.1 31.0 32.1 35.0 39.9
39 40 45 48 51 52
19 K 20 Ca 21
Sc 22
Ti 23
V 24
Cr 55
25
Mn 56
26
Fe 59
27
Co 59
28
Ni 64
29
Cu 65
30
Zn 70 73 75 79 80
31 Ga 32 Ge 33 As 34 Se 34 Br
84
36 Kr
39.1 40.1 45.0 47.9 50.9 52.0 54.9 55.8 58.9 58.7 63.5 65.4 69.7 72.6 74.9 79.0 79.9 83.8
86 88 89 91 93
37 Rb 38 Sr 39
Y 40
Zr 41
Nb 96
42
Mo 98
43
Tc 101
44
Ru 103
45
Rh 106
46
Pd 108
47
Ag 112
48
Cd 116
49 In
119 122 128 127
50 Sn 51 Sb 52 Te 53 I
131
54 Xe
85.5 87.6 88.9 91.2 92.9 95.9 98 101 103 106 108 112 115 119 122 128 127 131
133 137 139
55 Cs 56 Ba 57
La 178
72
Hf 181
73
Ta 184
74
W 186
75
Re 190
76
Os 192
77
Ir 195
78
Pt 197
79
Au 201
80
Hg 204
81 Ti
207 209
82 Pb 83 Bi
209 210 222
84 Po 85 At 86 Rn
133 137 139 178 181 184 186 190 192 195 197 201 204 207 209 209 210 222
223 226 227
87 Fr 88 Ra 89
Ac
223 226 227

Mass number of
major isotope
1 51 45 12
1H Major biosphere 23 V Biosphere trace 21 Sc Biosphere inactive Atomic 6C
1.01 element 50.9 45.0 number 12.0
element element
Relative
atomic mass

and to a lesser extent, sulphur and chlorine are electronegative. This has
consequences for the reactivity of biological molecules (Chapters 9, 11,
and 12) and for the formation of hydrogen bonds which leads to the
shapes of protein molecules (Chapter 12).
The size of atoms of the elements decreases on passing from left to
right and from bottom to top of the table. This means that hydrogen,
carbon, nitrogen, oxygen, and sulphur are all small elements. ­Carbon,
nitrogen, and oxygen are quite similar in size and so readily link together
in a range of biological molecules which almost always carry an outer
layer of tiny hydrogen atoms.

1.7 Electron Structure of Atoms

Section 1.4 discussed the structure of atoms which were found to con-
sist of a small, massive nucleus made up of protons and neutrons which
is surrounded by tiny, light electrons. The way in which the electrons
are arranged determines the properties of the atom and thus those of
the element. Electrons are organised into a series of energy levels, and
some simple rules govern their behaviour. The electrons are arranged
in levels of increasing energy called shells. The first, lowest-energy, Electrons in an atom
shell can hold one or two electrons; the second shell can hold between are arranged in shells of
increasing energy.
one and eight electrons; and the third electron shell can take up to

Elements, Atoms, and Electrons 


18 electrons­ but usually holds up to eight. An atom seeks to exchange
or share electrons with other atoms in order to achieve a complete outer
shell of electrons. This is because a full shell of electrons is very stable.
Higher energy levels are more reactive, and so only this outer shell of
electrons takes part in biochemical or chemical reactions.
Using these ideas, atomic structure diagrams can be drawn for each
element to show the electronic structure. When the number of electrons
in each shell is stated, starting with the number in the lowest-energy
shell, this is called the electronic structure of the element.

Worked Example 1.3


Oxygen is present in proteins, carbohydrates, and lipids. Give
the atomic structure diagram for oxygen, and state the electronic
structure.

Answer
From Table 1.4, oxygen has atomic number 8 and mass number 16.
Thus, it has 8 electrons and 16 – 8 = 8 neutrons.
The atomic structure diagram is drawn to show the number of
protons and neutrons in the nucleus and the electrons in shells,
2 in the first shell and 6 in the second as in Figure 1.1.
The electronic structure is O 2.6.

8p+
8n

= e–

Figure 1.1 Atomic structure diagram for oxygen.

Worked Example 1.4


Calcium occurs in the skeletons of many vertebrates. Give the
electronic structure for the element and construct an atomic struc-
ture diagram.

Answer
Calcium has atomic number 20 and mass number 40 (Table 1.5);
thus, it has 20 electrons and 40 – 20 = 20 neutrons.
The electronic structure is Ca 2.8.8.2.
The atomic structure diagram, Figure 1.2, shows the 20 ­protons
and 20 neutrons in the nucleus together with the four shells
of electrons.

 Chemistry for Life Sciences


20p+
20n

= e–

Figure 1.2 Atomic structure diagram for calcium.

O Ca

Figure 1.3 Simplified atomic structure diagram for oxygen and calcium.

The full atomic structure diagrams are often simplified to show only
the outer shell electrons around the element symbol which represents
the nucleus and inner full shells of electrons. In this way, the diagram
for oxygen (Figure 1.1) and calcium (Figure 1.2) are reduced to those
given in Figure 1.3.

Question 1.3
The element chlorine is implicated in the mechanism of nerve
impulses. Draw both full and simplified atomic structure diagrams
for it and give the electronic structure.

The atomic structure diagrams just described and the electronic


structures linked to them can be used to explain a range of interac-
tions between the atoms of different elements (Chapter 2). However,
these ideas do not always give results that correspond closely with
experimental observations. The approach of a theory called quantum
mechanics can be used to explain accurately the behaviour of elec-
trons in atoms. A discussion of the theory is beyond the scope of this
book: a full description is provided in Advanced Inorganic Chemistry
by ­Cotton et al. (1999). Parts of the volume of space around the nucleus
have different probabilities of being occupied by electrons. Regions
of high probability are called electron orbitals. Quantum mechanics An orbital is a volume of space
predicts a number of orbitals, and each one corresponds to a specific with a high probability of finding
an electron.
energy level for the electron.
In addition to the existence of orbitals, the theory predicts four impor-
tant features associated with them:

Elements, Atoms, and Electrons 


s-orbital p-orbital

= Atomic nucleus d-orbital

Figure 1.4 Atomic orbitals.

Figure 1.5 Two spin-paired electrons in an orbital.

1. There are several different types of orbital, each with a char-


acteristic shape. Three important types are labelled “s,” “p,”
s-orbitals and p-orbitals are and “d.” An s-orbital can be visualised as a sphere with an
important in biosphere elements. atomic nucleus at its centre (Figure 1.4). A p-orbital is shaped
like a dumbbell with the nucleus situated at the point where the
two lobes join (Figure 1.4). A d-orbital has four lobes, with the
nucleus placed at the centre of the cluster (Figure 1.4).
2. Each orbital can hold a maximum of two electrons. This idea
is known formally as the Pauli Exclusion Principle. Electrons
are regarded as having a property that can be interpreted
as spin, with each electron spinning either “clockwise” or
“anticlockwise.” When two electrons are present in an orbital,
the spins must be “paired,” with one spinning clockwise and the
other anticlockwise (Figure 1.5).
Orbitals are arranged in shells 3. The orbitals are arranged in a series of shells that increase in
within an atom. size and thus extend further from the atomic nucleus. The shells
are numbered sequentially 1,2,3, … . The energy of the shells
increases in the same sequence.
4. The electron shells can hold an increasing number of orbitals in
a fixed pattern as shown in Table 1.6. This confirms that there
are n2 orbitals in the nth shell and that the number of each type
of orbital increases in the sequence of odd numbers:
s,p,d,…   1,3,5,…

Table 1.6 Number and Type of Orbitals in Electron Shells of


an Atom
Total Number Orbital Type and Number
Shell of Orbitals s p d
1 1 1 0 0
2 4 1 3 0
3 9 1 3 5

10 Chemistry for Life Sciences


y

p-orbital

= Atomic nucleus

Figure 1.6 The three p-atomic orbitals.

The three p-orbitals are arranged mutually at right angles to one


another along the x, y, and z axes; they are called the px, py, and pz
­orbitals, respectively (Figure 1.6).
Within a shell, the orbitals occupy subshells where the orbitals are A subshell contains orbitals of
of equal energy. Thus, the three p-orbitals form a subshell as do the equal energy.
five d-­orbitals.
In the second shell, the four orbitals exist as a lower-energy subshell
with one s-orbital and a higher-energy subshell with three p-­orbitals of
equal energy. The third shell carries nine orbitals in three subshells, the
lowest-energy s-subshell with a single orbital, a higher-energy p-subshell
with three orbitals of equal energy, and a highest-energy d-subshell with
five orbitals of equal energy (Figure 1.7).
When electrons are added to the orbitals within an atom, they enter
in a fixed sequence; they occupy the orbitals of lowest available energy
first, and when a subshell of equal energy orbitals is present, they
occupy each orbital first before pairing in any one. This effect is known
as Hund’s Rule—it can apply when electrons enter p- or d-orbitals. The
sequence of electron occupancy of the two lowest-energy shells is shown Electrons always enter orbitals of
in Figure 1.8. The figure can be represented in a shorthand form as: lowest energy first.

1s22s22pX22py22pZ2
The number of electrons in an orbital is shown as a superscript
number­ after the orbital symbol. The second shell can hold up to eight
electrons when it is full, and then the structure is very stable. Elements

3d

Energy 3p

3s

Figure 1.7 The arrangement of orbitals in the third shell.

Elements, Atoms, and Electrons 11


2p
5 8 6 9 7 10

2s
3 4
Energy

1s
1 2

Figure 1.8 The sequence of electron occupancy of orbitals in shells 1 and 2.

with between one and seven electrons in the outer second shell will react
with other elements by gaining, losing, or sharing electrons in order to
Atoms like carbon try to gain a achieve a full shell or to leave it empty. This is the octet rule.
share in eight electrons for the
outer shell.
Principles 1 through 4 just described can be used to build up the
electronic structure, often called the electron configuration, of any
given element.

Worked Example 1.5


Draw a diagram to show the electron configuration of carbon.

Answer
From Table 1.4, carbon has atomic number 6 and therefore has six
electrons. The first two electrons occupy the 1s orbital, the next
two electrons enter the 2s orbital, the next electron enters the 2px,
and the last goes into the 2py. The energy level diagram is shown
in Figure 1.9.
It is important to note that the sixth electron goes into the 2py
and not the 2pX. The shorthand representation is
C 1s22s22px12py1

2p

2px 2py 2pz

2s
Energy

1s

Figure 1.9 Energy level diagram showing the arrangement of ­electrons


in the carbon atom.

12 Chemistry for Life Sciences


Question 1.4
Draw a suitable energy level diagram to show the electron con-
figuration of the oxygen atom.

Summary

All matter, including living organisms, is composed of elements.


Only a few of the naturally occurring elements are important in
the biosphere.
Each element is represented by a symbol and is made up of
many tiny atoms; in turn, an atom is formed from protons, neu-
trons, and electrons. The number of neutrons in the atoms of an
element can vary; the different forms are called isotopes. The
arrangement of electrons in an atom is determined by rules that
cause the electrons to be placed in orbitals, and these are organ-
ised into shells of increasing energy.

Suggested Further Reading

Atkins, P.W., and de Paula, J. (2006) Physical Chemistry, 8th ed., Oxford University
Press, Oxford.
Cotton, F.A., Wilkinson, G., Murillo, C.A., and Bochmann, M. (1999) Advanced
­Inorganic Chemistry, Wiley-Blackwell, Oxford.

End-of-Chapter Questions

Question 1.5 Write symbols for the elements boron, potassium, cobalt,
iodine, calcium, and molybdenum.
Question 1.6 For each of the following isotopes, 11 H, 21 H, 126 C, 15
31 P, and
37 Cl, give
17
(a) the relative atomic mass (Ar),
(b) the atomic number,
(c) the number of neutrons,
(d) the number of electrons.
Question 1.7 Draw simple electron structure diagrams to show the
electron arrangement in the elements
(a) sodium,
(b) boron,
(c) phosphorus.
Question 1.8 For the elements
(a) hydrogen,
(b) nitrogen,
(c) sodium,
(i) construct energy level diagrams to represent
the sequence of electron orbitals and shells in
the atom,
(ii) write the shorthand notation for the electron
configuration in each case.

Elements, Atoms, and Electrons 13


Covalent Bonding 2
and Molecules
2.1 Introduction

A living organism derives most of its character from the enormous range
of molecules contained within it. These help to determine the structure
of the body, the function of enzymes, the clotting of blood, cell respira-
tion, and innumerable other features. It is useful for us to understand the
structure of molecules and to consider the properties they show in order
to interpret the role they perform in the organism.

2.2 Interactions between Atoms

Proteins, sugars, and other important biological molecules are collec-


tions of atoms held together by a force of attraction called covalent Atoms share electrons to form
bonding. Covalent bonds are formed between atoms that can share covalent bonds.
electrons to achieve a full shell of electrons. Such a full shell is a
very stable structure. When two atoms move toward one another, the
outer-shell electrons in each rearrange themselves to reduce their poten-
tial energy. The energy falls to a minimum when they are a specific
distance apart. This distance, when measured between the two atomic
nuclei, is called the bond length. The fall in energy that has occurred is
the bond energy­ (Figure 2.1).

+
Potential Energy

– r

Distance between Nuclei

Figure 2.1 Potential energy change which occurs when two atoms are
brought together to form a chemical bond. The fall in energy E corresponds
to the energy of the chemical bond. The distance r between the nuclei of the
two atoms represents the potential energy minimum and is the bond length.

15
2.3 Covalent Bonds Are Formed by Sharing Outer Electrons

The simplest way to describe the formation of a covalent bond is to


consider the way in which the outer shells of electrons in the atoms
interact as the atoms approach one another. The outer shell of electrons
is often called the valence shell, so this description of covalent bond-
Only outer shell, valence shell, ing is called the valence-bond theory. The outer electrons interact by
electrons are shared in bonding. sharing themselves between the atoms to form overlapping full shells.
For example, the element hydrogen has one electron and needs to share
a second electron in order to give a full shell of two electrons. The
biologically significant elements carbon, nitrogen, oxygen, phosphorus,
sulphur, and chlorine all require a total of eight shared electrons to form
a full outer shell. The bonding process can be illustrated by the forma-
Electrons that form a bond are tion of the hydrogen molecule. Two hydrogen atoms each with one elec-
localised in the area between tron in the first shell (electron structure H 1) (Table 2.1) join together
the atoms.
so that the shells overlap and each shell gains a share in two electrons
(­Figure 2.2) and is full. The two atoms are linked strongly together to
form a hydrogen­ molecule. The two shared electrons are concentrated
in the volume of space between the two hydrogen nuclei to form the
covalent bond. The molecule is often shown as the two symbols for the
element linked by a line to indicate the bond, H–H, or more simply as
H2. The same ideas can be used to describe the formation of covalent
bonds in simple biological molecules.

Table 2.1 Names, Symbols, Electron Structure, and Valencies


(Oxidation Numbers) for Elements of Biological Importance
Name Symbol Electron Structure Valency
Hydrogen H 1 1
Carbon C 2.4 4
Nitrogen N 2.5 3 or 5
Oxygen O 2.6 2
Sodium Na 2.8.1 1
Magnesium Mg 2.8.2 2
Phosphorus P 2.8.5 3 or 5
Sulphur S 2.8.6 2
Chlorine Cl 2.8.7 1
Potassium K 2.8.8.1 1
Calcium Ca 2.8.8.2 2

H H H H

Two hydrogen atoms One hydrogen molecule H2

Figure 2.2 Formation of a covalent bond in the hydrogen molecule.

16 Chemistry for Life Sciences


Worked Example 2.1
The vital solvent medium in the living cell is water. Describe the
covalent bond in the water molecule, H2O.

Answer
Write the electronic structure for hydrogen and oxygen using the
data in Table 2.1:
H 1 O 2.6
Oxygen has six electrons in the outer shell and therefore needs
to share in two extra electrons to gain a full shell of eight.
Two hydrogen atoms are required to provide these two electrons.
Next, draw diagrams to show the outer-shell electrons of one
oxygen atom and two hydrogen atoms, and then allow the outer
shells of electrons to overlap (Figure 2.3).

H O H H O H

One oxygen atom and two hydrogen atoms One water molecule H2O

Figure 2.3 Formation of two covalent bonds in the water molecule.

Worked Example 2.2


Methane, CH4, is the simplest organic compound; it is the starting
point for understanding the complex range of biological molecules.
Use diagrams to construct the covalent bonds in methane.

Answer
Write the electronic structure for carbon and hydrogen using the
data in Table 2.1:
C 2.4 H 1
Carbon has four electrons in the outer shell. To form a full outer
shell of eight electrons and thus achieve a stable structure, it needs
to gain a share in four electrons.
Four hydrogen atoms are required to provide these electrons.
Thus, the formula is confirmed as CH4.
Now draw a carbon atom and four hydrogen atoms showing only
the outer-shell electrons. Bring the atoms together allowing the
outer shells to overlap in a diagram of the molecule (Figure 2.4).
The water and methane molecules can be shown in the same
simplified form as the hydrogen molecule with lines to indicate
the bonds.

Covalent Bonding and Molecules 17


H

H C H
H

H H

The structural formula of


methane.
H C H H C H

H
H

One carbon atom and four hydrogen atoms One methane molecule CH4

Figure 2.4 Formation of the methane molecule with four covalent bonds.

Question 2.1
Amino acids are derived from the ammonia molecule, NH3.
Draw diagrams to show how the covalent bonds in the molecule
are formed, and write a simplified form of the structure to show
the bonds.

Question 2.2
Sulphur bacteria use the compound hydrogen sulphide, H2S, to
provide hydrogen for the reduction of carbon dioxide to form
­sugars. Draw diagrams to explain how covalent bonds are formed
in the hydrogen sulphide molecule.

The form of the methane and water molecules was achieved by atoms
sharing electrons in pairs to give covalent bonds. It is possible for a pair
of atoms to share more than one pair of electrons to form two or three
covalent bonds.
Oxygen, O2, which is vital for the process of respiration, is an impor-
tant example of a molecule that shares two pairs of electrons between the
atoms. The electronic structure of the oxygen atom is O 2.6 (Table 2.1).
Thus, it requires a share in two extra electrons to give a full outer shell.
These can be supplied by a second oxygen atom that, in turn, shares two
electrons from the first atom. This is conveniently shown by a diagram
of the oxygen atoms and the oxygen molecule formed (Figure 2.5). The
molecule is represented in a simple form by linking the element symbols­
by two lines: O=O.

O O O O

Two oxygen atoms One oxygen molecule O2

Figure 2.5 Double covalent bond formation in the oxygen molecule.

18 Chemistry for Life Sciences


Worked Example 2.3
The gaseous respiration product carbon dioxide, CO2, is a covalent
molecule. Draw diagrams to show the formation of the carbon–
oxygen bonds.

Answer
First, write the electron structures of carbon and oxygen
C 2.4 O 2.6 (Table 2.1).
Next, draw diagrams to show the outer shell electrons for one
carbon and two oxygen atoms.
Carbon, with four outer-shell electrons, requires a share in four
more to give a full shell of eight. These are provided by two oxygen
atoms, each giving two electrons. The oxygen atoms gain, at the
same time, a share in two electrons to increase their six electrons
to a full shell of eight.
Finally, allow the three atoms to come together with overlap of Diagrams showing overlap of
the outer shells of the electrons (Figure 2.6). outer-shell electrons are used to
explain covalent bonding.
The simple representation of the carbon dioxide molecule is
O=C=O.

O C O O C O

Two oxygen atoms and one carbon atom One carbon dioxide molecule CO2

Figure 2.6 Double covalent bond formation in the carbon dioxide


molecule.

Question 2.3
Nitrogen gas, N2, is the main component of the earth’s atmosphere.
It provides the ultimate source of nitrogen for amino acids and
proteins. Draw diagrams to show how multiple covalent bonding
occurs in the nitrogen molecule.

2.4 Formulae of Compounds

In discussing the formation of covalent bonds, it has been useful to write


the formulae for molecules using element symbols. It was clear that the
number of electrons needed by each element to complete its outer shell
determined the ratio of the element within the given molecule. When
we consider the same element in different molecules, it always requires
a share in the same number of extra electrons. Thus, hydrogen always
shares one electron, carbon requires four electrons, and oxygen needs
two electrons. The number shared is often called the valency or combin- The number of outer-shell
ing power of the element. More formally, it is known as the oxidation electrons shared by an element
in bonding is the valency.
number. These valencies can be used conveniently to determine the

Covalent Bonding and Molecules 19


Simple rules are used to formulae of compounds in a simple way, without the need to consider
determine the formula of a outer electron shell structures.
compound from the valency.
In order to write the formula of the water molecule, the symbols and
valencies for the elements are used.

Worked Example 2.4


Write the formula for the water molecule.

Answer
Water contains the elements hydrogen and oxygen.
Write the symbols H O
Write the valency for each element (Table 2.1) 1 2
Change the valency of each element to the
other one, writing the numbers below the line
and after the element symbols H2 O1
Close up the numbers and letters, ignore the
number 1 to give the formula H 2O

Worked Example 2.5


Give the formula for the methane molecule.

Answer
Methane contains the elements carbon and
hydrogen. C H
Write the valency for each element (Table 2.1) 4 1
Change over the valencies from one element to
the other and write below the line and after the
element symbol C1 H4
Close up and ignore the number 1 to obtain the
formula CH4

Worked Example 2.6


Determine the formula of the carbon dioxide molecule.

Answer
Carbon dioxide contains the elements carbon and oxygen.
Write the symbols C O
Write the valency for each element 4 2
Exchange the valencies from one element to the
other, writing each below the line after the symbols C2 O4
In this case, the numbers can be simplified by
dividing by two before closing up to give the formula;
when the numbers obtained initially can be simplified
by dividing by a common value, then this is usually
carried out CO2

20 Chemistry for Life Sciences


Question 2.4
Use valencies to write the formula of ammonia, which contains
the elements nitrogen and hydrogen.

Question 2.5
Determine the formula for hydrogen sulphide, containing hydro-
gen and sulphur, by using element valencies.

When a compound contains more than two elements, the same ideas Groups of atoms as well as
can be used to determine the formula. The process is often made simpler single atoms can have a valency.
because groups of atoms usually stay together in a number of different
compounds. Thus, the carbonate group containing a carbon atom and
three oxygen atoms, CO3, occurs in many compounds such as calcium
carbonate, CaCO3; sodium carbonate, Na2CO3; and magnesium carbon-
ate, MgCO3. In each case, the valency of two can be assigned to the
carbonate group and the formula determined on this basis. A selection
of these groups and valencies is collected in Table 2.2.

Table 2.2 Names, Symbols, and Valencies for Some Biologically


Significant Groups
Group Formula Valency
Amide CONH2 1
Amine NH2 1
Ammonium NH4 1
Carbonate CO3 2
Carboxylic acid COOH 1
Bicarbonate (hydrogen carbonate) HCO3 1
Hydroxide OH 1
Alcohol OH 1
Ketone CO 2
Sulphate SO4 2
Phosphate PO4 3

Worked Example 2.7


Calcium carbonate is a major component of the exoskeleton of
phytoplankton species. Use valencies to determine the formula of
calcium carbonate.

Answer
Calcium carbonate contains the element calcium
and the carbonate group (Table 2.2). Ca CO3
Write the valency for each (Table 2.1 and
Table 2.2). 2 2

Covalent Bonding and Molecules 21


Change valency for element to the group and
vice versa; write below the line and after the symbol. Ca2 CO3 2
Simplify the numbers by dividing by two; the
resulting 1s are not written; close up symbols to give
the formula. CaCO3

Worked Example 2.8


Ammonium carbonate is formed when the products of protein
decay, ammonia, and carbon dioxide dissolve in water. What is
the formula for ammonium carbonate?

Answer
Ammonium carbonate contains the groups ammonium and
­carbonate (Table 2.2). NH4 CO3
Interchange the valencies between the groups, 1 2
write below the line and after the formula NH4 2 CO3 1
Close up the group formulae, omitting the one
and placing a bracket around the NH4 in order to
avoid reading the four and two as forty-two and
to show that there are two NH4 groups, and not
just two H4 groups (NH4)2CO3

Worked Example 2.9


Calcium phosphate is an important mineral in the structure of
bone. Find the formula of calcium phosphate.

Answer
Calcium phosphate contains the element calcium and the
phosphate group (Table 2.2). Ca PO4
Exchange valencies with one another and write 2 3
after the symbol or formula and below the line
Place the group formula, PO4, in a bracket and
close up to give the formula of the compound Ca3(PO4)2

Question 2.6
Determine the formula of potassium sulphate, which is a source of
soluble potassium for the biosphere. The compound contains the
sulphate group (Table 2.2).

Question 2.7
Use valencies to find the formula of the fertiliser ammonium
phosphate, which contains the ammonium and phosphate groups
(Table 2.2).

22 Chemistry for Life Sciences


2.5 Covalent Bonds Formed by Combining Atomic Orbitals

The formation of covalent bonds by the sharing of electrons between


atoms was discussed in Section 2.3. It was seen that this description of
molecules was quite simple. Only a few electrons were involved and the
results were easy to obtain and understand. However, a number of mole- Explaining covalent bond
cules do not have the properties that would be expected from a valence- formation by sharing of valence
shell electrons is not always
bond description. For example, the oxygen molecule is very reactive as satisfactory.
is clear from its role in respiration. This reactivity can be ascribed to
a presence of two electrons in the molecule which are unshared. They
do not form a pair as is expected by the overlap of outer-shell electrons
to form electron pairs. This means that a more appropriate theory is
needed to explain the behaviour of oxygen and many other molecules
that possess unexpected properties.
In discussing a new approach to the electron structure of molecules,
it is important that the ideas of valence-bond theory not be abandoned.
They can continue to be used whenever they provide a suitable descrip-
tion of a molecule. It is normal to pick out the best theory for use with
any example.
The idea of atomic orbitals was considered in Section 1.7; it can be Molecular orbitals are formed by
extended to describe orbitals within molecules. Several of the same a combination of atomic orbitals.
rules apply to molecular orbitals as to atomic orbitals:
• Molecular orbitals are occupied by electrons in order of increas- Molecular orbitals are filled with
ing energy. electrons using the same rules
as atomic orbitals.
• Each molecular orbital can hold up to two electrons.
• When two or more molecular orbitals have the same energy,
electrons enter each orbital singly before pairing in any one.
The formation of molecular orbitals can be illustrated by the inter-
actions that take place when two isolated atoms with atomic orbitals
approach one another until the orbitals overlap. In the case of the hydro-
gen molecule, two hydrogen atoms, each with a 1s atomic orbital, move
together and overlap to produce two new molecular orbitals (Figure 2.7).
Although the two atomic orbitals were the same, the two molecular
orbitals are quite different. They have different shapes: one is concen-
trated mainly in the space between the two hydrogen nuclei, and the
second consists of two parts or lobes that are distributed away from the
space between the nuclei. The first orbital is of lower energy than either
of the original atomic orbitals, and the second is of higher energy than
Second molecular orbital

Molecular orbital
Two 1s atomic orbitals Two overlapping One hydrogen molecule H2
1s atomic orbitals

Figure 2.7 Overlap of two hydrogen atomic orbitals to form two hydrogen
molecular orbitals and thus a covalent bond.

Covalent Bonding and Molecules 23


Antibonding
molecular orbital

Energy

Bonding
molecular orbital

Hydrogen Hydrogen Hydrogen


atom H molecule H2 atom H

Figure 2.8 Molecular orbital energy level diagram for the formation of a
hydrogen molecule from two hydrogen atoms.

the atomic orbitals. The average energy of the two molecular orbitals is
the same as the average energy of the two atomic orbitals.
Two electrons are available to occupy the molecular orbitals. One
electron is supplied by each hydrogen atom. The electrons enter the
molecular orbital of lowest energy, form a pair, and fill it. This can be
shown on a molecular orbital energy level diagram (Figure 2.8).
Placing the two electrons in the low-energy molecular orbital con-
centrates them in the region of space between the two atomic nuclei.
It causes a covalent bond to be formed. This orbital is called a bonding
molecular orbital. The second, higher-energy molecular orbital, if it
held electrons, would localise them away from the space between the
nuclei. The nuclei would be unshielded from one another and would
Molecular orbitals can be of low repel and no bond would be formed. This is called an antibonding
energy (bonding) or high energy molecular orbital.
(antibonding).
The idea used here to describe the formation of a covalent bond in a
molecule using molecular orbitals formed from atomic orbitals is called
the molecular orbital theory. It can be seen that both valence bond and
molecular orbital theory can give the same results—that is, the forma-
tion of a covalent bond by concentrating electron density between the
centres of two atoms. But the two theories have arrived at the result by
different methods.

2.6 Single Overlap, the Sigma-Bond

For the hydrogen molecule, molecular orbitals were formed by the over-
lap of two spherical 1s atomic orbitals. From Figure 2.7 it can be seen
that the two atomic orbitals have approached each other along a line
joining the centres of the two atoms to give a single region of ­overlap.

24 Chemistry for Life Sciences


Single overlap Single overlap

s atomic p atomic p atomic p atomic


orbital orbital orbital orbital

Figure 2.9 Single overlap of s and p or p and p atomic orbitals in covalent


bond formation.

An s-orbital can overlap with a px-orbital in the same way to give a ­single
region of overlap (Figure 2.9) and thus form two molecular ­orbitals. Two
px-orbitals can interact by the same process to form, once more, a single
region of overlap (Figure 2.9).
The formation of bonding and antibonding molecular orbitals by
­single overlap is indicated by placing the Greek letter sigma, σ, in
front of the orbital name. In Figure 2.9, the two molecular orbitals then
become written as σ-bonding molecular orbital and σ-antibonding
molecular orbital. The word “bonding” is usually left out and the term
“antibonding” is replaced by the asterisk (*).
Thus, the two molecular orbitals are simplified to σ-molecular
orbital and σ*-molecular orbital. In general, any covalent bond formed Single overlap of atomic orbitals
by single overlap is called a σ-bond. gives a single σ-bond.

2.7 Double Overlap, the Pi-Bond

The three p-orbitals are arranged along the x, y, and z axes (Section 1.7).
Single overlap occurs when two px atomic orbitals approach each other
along the x-axis, which is the line joining the centres of the two atoms.
When two py- or two pz-orbitals approach each other along the x-axis,
a different type of overlap takes place. The lobes of the p-orbitals over-
lap sideways in two regions rather than one. The overlap occurs above
and below the line joining the two atomic centres (­Figure 2.10). The
overlap of two p atomic orbitals leads to the formation of two molecu-
lar orbitals: a low-energy bonding molecular orbital and a high-energy

Double
overlap

Double
overlap

Two pz atomic orbitals Two py atomic orbitals

Figure 2.10 Sideways interaction of pz and pz or py and py atomic orbitals to


give double overlap.

Covalent Bonding and Molecules 25


π-antibonding
molecular orbital

Double
overlap

pz atomic pz atomic Sideways double π-bonding molecular


orbital orbital overlap of two pz orbital
atomic orbitals π-molecular orbitals

Figure 2.11 Sideways overlap of two p atomic orbitals to form two


π molecular orbitals and a covalent bond.

antibonding molecular orbital. The bonding molecular orbital con-


sists of two lobes: one above and one below the centre-line of the new
molecule­. The ­antibonding molecular orbital is composed of four parts
that are directed away from the region between the atoms (­Figure 2.11).
It is important to bear in mind that double overlap can occur only after
single overlap has taken place.
Double overlap in the formation of two molecular orbitals is indicated
by placing the Greek letter pi, π, before the orbital name. Thus, the molec-
ular orbitals in Figure 2.11 are written as π-bonding ­molecular orbital
and π-­antibonding molecularorbital, or more briefly as π-molecular
Double overlap of atomic orbitals orbital and π*-molecular orbital. A covalent bond formed by double
gives a π-bond. overlap is called π-­bond.Thus, it can be stated that a σ-bond is always
formed before a π-bond. Molecular orbitals are filled by electrons in
order of increasing energy. This order is:
σ < π < π* < σ*
When two molecular orbitals have the same energy, then electrons
will enter each orbital singly before forming pairs in any one.
pz atomic
orbital py atomic
orbital

O H O H

Single σ-bonds

H
s atomic
orbital
One oxygen and two hydrogen atoms Water molecule

Figure 2.12 Overlap of atomic orbitals in hydrogen and oxygen atoms to


form ­covalent σ-bonds in the water molecule.

26 Chemistry for Life Sciences


2.8 Molecules with σ- and π-Bonds

The hydrogen molecule, H2, contains a single σ-bond, formed by the


overlap of two s-atomic orbitals (Section 2.5). In the water molecule,
two p-atomic orbitals in oxygen, each overlap with an s-atomic orbital
in hydrogen to form two single σ-bonds. This is shown in Figure 2.12.
The oxygen molecule, O2, contains both σ- and π-bonds. The forma- An energy level diagram can be
tion of these bonds can be understood best by constructing the energy used to show the formation of
σ- and π-bonds.
level diagram.

Worked Example 2.10


Use a molecular orbital diagram to show the bond formation in the
oxygen, O2, molecule.

Answer
Write the electron configuration of the oxygen atom (Chapter 1).
O (1s)2 (2s)2 (2px)2 (2py)1 (2pz)1
Draw the molecular orbital energy level diagram for the two
oxygen atoms and the oxygen molecule.
Place the available electrons in the molecular orbitals, filling
the lowest energy orbitals first and putting the electrons singly into
­orbitals of the same energy before pairing in any one (­Figure 2.13).
From the diagram (Figure 2.13), it can be seen that the eight
available 2p electrons occupy a σ-bonding molecular orbital, two
π-bonding molecular orbitals, and two antibonding molecular
­orbitals (one electron in each). Thus, there are a total of six elec-
trons in bonding molecular orbitals. The antibonding molecular
orbitals contain a total of two electrons.
σ*

π* π*

Energy

2px 2py 2pz 2pz 2py 2px

π π

2s 2s
Oxygen atom O Oxygen molecule O2 Oxygen atom O

Figure 2.13 Molecular orbital energy level diagram to show the


­formation of the oxygen molecule O2 from two oxygen atoms.

Covalent Bonding and Molecules 27


When electrons are present in bonding molecular orbitals, they cause
attraction between the atoms. But, electrons in antibonding molecu-
lar orbitals cause repulsion between the atoms. Thus, to determine the
number of bonds in the oxygen molecule, the number of electrons in
antibonding orbitals is subtracted from the number in bonding orbit-
als. Six electrons minus two electrons gives four electrons. Each bond
requires two electrons, so the number of bonds in the oxygen molecule
is four divided by two, giving two bonds.
This can be summarised as follows:
Electrons in bonding molecular orbitals =6
Electrons in antibonding molecular orbitals =2
Bonding minus antibonding electrons 6–2=4
Number of bonds (two electrons in each bond) 4÷2=2
The single (that is, unpaired) electrons in the π*-orbitals give the
oxygen molecule its high reactivity.

Question 2.8
Construct the molecular orbital energy level diagram for the nitro-
gen molecule, N2, to show the σ- and π-bonds.

In forming covalent bonds, hydrogen uses only a 1s orbital to form a


single σ-bond with other elements. The elements carbon, nitrogen, and
oxygen use 2s and 2p atomic orbitals to form single σ-bonds and double
or triple π-bonds. The heavier elements phosphorus and chlorine use 3s
and 3p atomic orbitals to form mainly σ-bonds, although phosphorus
forms double π-bonds, especially with oxygen.

2.9 Hybrid Molecular Orbitals

Explaining the bonds in molecules by the use of molecular orbitals has


helped us to understand the properties of compounds. However, a num-
ber of characteristics of molecules still remain hard to interpret. Thus,
the angle formed by H-O-H bonds in water is known to be 105°. The
description of the molecule in Section 2.8 suggests a bond angle of 90°.
A development of molecular orbital theory called hybridisation can be
used to explain this anomaly and others like it.
Hybridisation can be justified by considering the overlap of hydrogen
1s and oxygen 2p orbitals shown in Figure 2.12. Only a small part of
each 2p orbital takes part in overlap; one lobe in each orbital remains
unused. Because the strength of a bond is proportional to the degree of
A 2s orbital and three 2p orbitals overlap, this picture suggests a weak bond. The overlap is increased and
can combine together to form the bond made stronger by modifying, or hybridising, the orbitals on
four equal sp3 hybrid orbitals,
and this leads to strong oxygen. The single 2s orbital combines with the three 2p orbitals to give
covalent bonds. four new hybrid orbitals called sp3 hybrids.
These four hybrid orbitals are equal, and each consists of one large
lobe and one very small lobe (Figure 2.14). The sp3 hybrid orbitals are
arranged tetrahedrally around the oxygen atom. They each use the
large lobe for overlap and form strong bonds. Thus, it is energetically

28 Chemistry for Life Sciences


Figure 2.14 An sp3 hybrid orbital.

Lone pair
electrons

σ-bond σ-bond
O

H H

Lone pair electrons

Figure 2.15 Overlap of two hydrogen atomic s orbitals with two oxygen
sp3 hybrid orbitals to form two σ-bonds. Two sp3 hybrid orbitals each contain
a pair of unshared electrons and form lone pairs.

f­ avourable for oxygen to use hybrid orbitals in forming the water mol-
ecule. The six available electrons in oxygen occupy each sp3 hybrid
singly before pairing in two of the orbitals. For water, the overlap of
orbitals is shown in Figure 2.15, with the small lobe on each hybrid
left out for clarity. The H-O-H bond angle predicted by this theory is
the tetrahedral angle, 109°, a little larger than the 105° found in the
actual molecule. The difference is explained by the strong repulsion
between the two pairs of unshared electrons which pushes them apart
and reduces the H-O-H angle to 105°.
The unshared pairs of electrons in two of the sp3 hybrid ­orbitals occupy
a significant region of space. Each protrudes out from the ­oxygen atom
and is called a lone pair of electrons. The formation of hybrid orbitals is Hybrid orbitals not used to form
important in describing the bonds formed by carbon and nitrogen as well covalent bonds contain unshared
electron pairs called lone pairs.
as oxygen. Such lone pairs on oxygen or nitrogen atoms are important in
determining the solvent power of water (Chapter 5).

Worked Example 2.11


Draw hybrid orbitals to show the formation of four σ-bonds in the
methane molecule CH4.
Answer
Write the electronic structure of the carbon atom:
C (2s)2 (2px)1 (2py) 1
The 2s, 2px, 2py, and the unoccupied 2pz orbitals form four
equal sp3 hybrid orbitals.
The four available electrons on carbon (the 1s electrons remain
unused) occupy each hybrid orbital singly.

Covalent Bonding and Molecules 29


Four hydrogen atoms each provide a 1s orbital with a single elec-
tron for overlap with the sp3 hybrids to give four equal σ-bonds.
Draw the diagram to show the orbitals and the bonds
(Figure 2.16).

σ-bond
C

H H

Figure 2.16 Overlap of four hydrogen atomic s orbitals with four


­carbon sp3 hybrid orbitals to form four σ-bonds.

Summary

When two atoms share between them a pair of electrons, a cova-


lent bond is formed. Atoms of elements share electrons in order to
achieve a full outer shell that is stable. Hydrogen requires a share
in two electrons, but carbon, nitrogen, and oxygen each require a
share in eight. A full outer shell may be formed by sharing two or
three pairs of electrons in some cases. The number of electrons an
element can share is the valency. Valencies are used to determine
the formulae of compounds.
The formation of covalent bonds can also be explained by the
overlap of atomic orbitals to form molecular orbitals. Energy level
diagrams are drawn to show the changes in energy which occur on
bond formation. Single overlap of atomic orbitals gives σ-bonds
and double overlap gives π-bonds. Bonding and antibonding
molecular orbitals are formed by the overlap of atomic orbitals.
The combination of s and p atomic orbitals gives rise to hybrid
orbitals in a number of molecules. Hybrid orbitals form strong
bonds and lead to the identification of lone pair electrons.

30 Chemistry for Life Sciences


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