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Chemistry
for the Life Sciences
Second Edition
Chemistry
for the Life Sciences
Second Edition
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Contents
Preface xi
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
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
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
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
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
Index 249
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.
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.
Raul Sutton
Bernard Rockett
Peter Swindells
Preface xiii
Elements, Atoms, 1
and Electrons
1.1 Introduction
1.3 Atoms
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.
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;
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.
Answer
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.
Question 1.2
Write an equation to represent the β-decay of the radioactive
35 S.
isotope 16
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.
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
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–
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.
= e–
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.
p-orbital
= Atomic nucleus
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
2s
3 4
Energy
1s
1 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.
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
2s
Energy
1s
Summary
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.
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.
+
Potential Energy
– r
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
H H H H
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
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.
H C H
H
H 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
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
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.
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
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
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
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.
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
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
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).
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.
Energy
Bonding
molecular orbital
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.
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.
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.
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
Double
overlap
O H O H
Single σ-bonds
H
s atomic
orbital
One oxygen and two hydrogen atoms Water 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
π π
2s 2s
Oxygen atom O Oxygen molecule O2 Oxygen atom O
Question 2.8
Construct the molecular orbital energy level diagram for the nitro-
gen molecule, N2, to show the σ- and π-bonds.
Lone pair
electrons
σ-bond σ-bond
O
H H
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).
σ-bond
C
H H
Summary
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