ATOMIC STRUCTURE

A Development of Ideas
✓ The atom was first suggested by Greek philosopher Democritus, who believed that an atom was the
smallest particle that could not be split any further. Since then, the model of the atom has been
developed into the one we use today.
 Atomos = unsplittable

✓ Aristotle and Plato who were more influential disagreed with Democritus’s view and the ideas of
atoms disappeared for about 1500 years

✓ During the 17th century early scientists like Boyle and Hooke stared to explain the behaviour of gases
in terms of particles or ‘corpuscles’.

✓ In the 1806, Dalton proposed that

• Each element has its own type of atom which differs in mass and size from the
atoms of other elements
• Atoms are not created or destroyed during chemical reactions
• When elements form compounds their atoms combine in a simple ratio to form
‘molecules’.
• Atoms in his model were tiny and indivisible called atoms

✓ During the 19th century work on electricity and electrolysis by Faraday indicated that atoms were
probably not simple ‘snooker ball’ like objects but were probably made from simpler particles which
were electrical in nature.

✓ In 1897, Thomson discovered the first sub-atomic particle — the electron. Thomson
proposed the plum pudding model where negatively charged electrons move in a
‘sea’ of charge in a positively charged atom

✓ In 1909 Millikan measured the actual mass and charge of the electron.
Mass: 1/2000 Charge: -1

✓ In 1911, Rutherford carried out experiments to find that most of the mass of an
atom is concentrated in the center, where negatively charged electrons orbit the
central positively charged nucleus. The positive and negative charges balance to
make the atom neutral.

✓ In 1913, Bohr suggested that electrons orbit the nucleus on paths. Bohr’s planetary
model provided an explanation for the difference in energy of electrons at different
distances from the nucleus.
The Structure of the Atom
An atom is the smallest particle of an element.

Atoms are made up of three types of sub-atomic particles — protons, neutrons, and electons.
• Protons and neutrons, also called nucleons, make up the nucleus.
They are found at the center of an atom where most of the mass is concentrated
• Electrons orbit the nucleus in shells and do not contribute much to the mass of the atom

Particle Particle Relative Mass Relative Charge

Proton 1 1
Neutron 1 0
Electron 1/1840 -1

• Element, X
• Mass number, A, is the total number of protons and neutrons in the
nucleus
• Atomic number, Z, is the number of protons. The number of positively
charged protons is equal to the number of negatively charged electrons in
an atom, making the atom neutral

Mass Number A
Number of protons + Number of neutrons

Atomic Number
Atomic Number = Number of protons = number of electrons

Atomic Number

• It fixes the identity of an atom, i.e. which element it is. E.g. the element with 8 protons must
be oxygen
• It fixes the position of the element in the periodic table. Elements are arranged in order of
atomic number.
• It determines the properties of the element
 Isotopes
Atoms of the same element can have different numbers of neutrons, and therefore different
masses — these are called isotopes.

Isotopes
Atoms with the same number of protons and a different number of
neutrons.

• Isotopes have different mass numbers but the same

atomic number because atoms of the same element
must have the same number of protons.
• Isotopes of the same element have the same electronic
configuration so react in the same way in chemical
reactions.
• Because isotopes have different masses they have small
differences in physical properties, e.g. melting point,
boiling point and density.
• Isotopes can only be separated using the differences in
physical properties.

Mass Spectrometry
A method of separating and identifying particles according to their masses

• Measures the masses of atoms and molecules.

• It can be used to identify the isotopes in an element
• It can be used to measure the masses of molecules and the fragments into which molecules can
be broken

N.B Mass spectrometry can be used to provide structural information, identify an unknown
compound, or determine the relative abundance of each isotope of an element.
 Time-of-Flight Mass Spectrometer
• A Time-of-Flight Mass Spectrometer works by accelerating an ionised sample and calculating mass per
charge based on how long each ‘object’ is in flight for. Since every ‘object’ receives equal force the
acceleration of each ion will be inversely proportional to its mass.

• The sample is first ionised by bombarding it with electrons, which also causes fragmentation to form
smaller groups of atoms.

• Ions tend to have +1 charge, since a bombarding electron will knock an electron out of an atom’s shell,
so ‘mass per charge’ can generally be taken as simply ‘mass’.

• The ions are then accelerated by Electromagnetic Field and travel through a vacuum area called
the Drift Region, before being detected by the Ion Detector

The mass spectrum for zirconium

The number of isotopes

The 5 peaks in the mass spectrum shows that there are 5 isotopes of zirconium - with
relative isotopic masses of 90, 91, 92, 94 and 96 on the 12C scale.

The abundance of the isotopes

The relative abundances are given as percentages. Again you can find these relative
abundances by measuring the lines on the stick diagram.
In this case, the 5 isotopes (with their relative percentage abundances) are:
zirconium-90 51.5
zirconium-91 11.2
zirconium-92 17.1
zirconium-94 17.4
zirconium-96 2.8
Working out the relative atomic mass
Suppose you had 100 typical atoms of zirconium. 51.5 of these would be 90Zr, 11.2
would be 91Zr and so on.
Note: If you object to the idea of having 51.5 atoms or 11.2 atoms and so on, just assume
you've got 1000 atoms instead of 100. That way you will have 515 atoms, 112 atoms, etc.
Most people don't get in a sweat over this, and just use the numbers as they are!
Relative atomic mass(RAM)

• the ratio of the average mass of one atom of an element to one twelfth of the mass of an
atom of carbon-12(1/12 of the mass of the 12C atom)
• Isotopes of the same element have different numbers of neutrons, so you need to calculate
for one specific isotope.
• atomic mass of oxygen is 16 u means that one atom of oxygen is 16 times heavier than
1/12 of a carbon-12 atom.
• The average mass of one atom of an element in the naturally occurring mixture of
isotopes relative to 1/12 of the mass of the 12C atom
• Because RAM is an average value it is not usually a whole number
• The RAM of an element can be calculated if we know the abundances and mass numbers
of its isotopes.

Isotopic Mass

• The exact relative mass of an atom of a specific isotope of an element including the
electrons.
• This is almost identical to the mass number.
• e.g O16 has an exact relative mass of 15.994915

Wave Nature of the Electron

• De Broglie showed that a beam of electrons could undergo diffraction. This can only
occur with waves (like light).
• Electrons can act as particles and waves

Quantum Mechanics
• Bohr’s model did not work as it assumes the electron is a particle and moves in definite
orbits.
• We now know that the electron has wave properties and ‘uncertainty’.
• The ideas were taken into account in the new science of quantum mechanics.
• This treats the electron as a wave and attempts to calculate where in the atom the
electrons are probably located.
• We can never say exactly where an electron is, we can only say where it is likely to be
found
Electron Shells
Electrons orbit the central nucleus in shells. Each shell can hold a different number of electrons.

Each shell can hold 2n2 electrons, where n is the principal quantum
number — this is the shell number or energy level number.
n Shell Number of Electrons
1 1st 2(1)2 = 2
2 2nd 2(2)2 = 8
3 3rd 2(3)2 = 18
4 4th 2(4)2 = 32

Atomic Orbitals and Sub-Shells

Electron shells are made up of atomic orbitals, which are regions in space where electrons may be
found. Each shell is composed of one or more orbitals and each orbital can hold one pair of electrons.
There are four main types of orbitals: s-, p-, d-, and f-.

The s-orbitals are spherical and can hold up to two electrons.

The p-orbitals have a three-dimensional dumbbell shape and can hold up to

two electrons each, but they always come in groups of three of the same
energy, meaning up to six electrons can be held. These p-orbitals are named
px, py, and pz.

The d-orbitals are more complex in shape. d-orbitals can hold up to two electrons each, but they
always come in groups of five of the same energy, meaning they can hold a total of ten electrons.
The F-orbitals are which can contain 7 pairs of electrons.
 Within each shell, orbitals that are of the same energy level are grouped together in sub-shells.

Sub-Shell 1s 2s 2p 3s 3p 3d
Orbital s s p p p s p p p d d d d d
Electrons 2 2 2 2 2 2 2 2 2 2 2 2 2 2
Total Electrons 2 8 18

Electrons and Spin

Electrons have an intrinsic property called spin that is caused by the two negative charges of electrons
in an orbital repelling each other.

The spin of an electron can be either up or down.

For two electrons in the same orbital, the spins must be

opposite to minimise the repulsion.

Electrons are represented by arrows pointing up

(spin up) or pointing down (spin down) to show the different directions of spin.

Energy Levels
Only one type of atomic orbital makes up a sub-shell. Each sub-shell has a different energy level.

The lowest energy levels correspond to s-orbitals as they are closest to the nucleus. The highest
energy levels correspond to f-orbitals as they are the furthest from the nucleus.

Note that 4s is lower in energy than 3d, so 4s will fill first.

Electron Configuration
Shells and sub-shells are filled with electrons according to a set of rules:

 Atomic orbitals with the same energy are occupied individually first before pairing
 The lowest available energy level is filled first
 No more than two electrons can fill an atomic orbital
Electron configuration is represented by a specific notation.

Electron Configuration

nxy
n principal quantum number
x type of orbital, e.g. s, p, d, f
y number of electrons in the orbitals of the
subshell

Electron configurations can be simplified by using the shorthand notation — the noble gas that
comes before the desired element is written in square brackets and then the electrons that come
after are written using the general notation.

For example, potassium has 19 electrons. The full electron configuration is written as:

1s22s22p63s23p64s1

The electronic configuration of potassium can be simplified using the shorthand notation:

[Ar]4s1
 Worked Example: Electron Configuration of Atoms Write

the electron configuration of Ca.

Solution
1. Determine the number of electrons in the atom — the
number of electrons in the atom is equal to its atomic
number on the Periodic Table:
Ca has 20 electrons

2. Use the rules to fill up the sub-shells:

4s is lower in energy than 3d, so 4s will fill first.

3. Write the electron configuration:

The full electron configuration is 1s22s22p63s23p64s2
The shorthand notation is written as [Ar]4s2

Worked Example: Electron Configuration of Ions Write

the electron configuration of Mg2+.

Solution
1. Determine the number of electrons in the atom: Mg
has 12 electrons
Mg loses 2 electrons to form Mg2+, therefore, Mg2+ has 10
electrons
2. Use the rules to fill up the sub-shells:

3. Write the electron configuration:

The full electron configuration is 1s22s22p6

The shorthand notation can be written as [Ne]

Remember the 4s-orbital is lower in energy than the 3d-orbital. Therefore, the 4s-orbital will fill \
first, before the 3d-orbita
 1st Ionisation Energy

The energy needed to remove one electron from each atom in one mole of gaseous
atoms of an element.

It is the energy needed for the process:

M(g) → M+(g) + e
The 1st I.E. for an element will depend on:

a) The charge on the nucleus

b) The effect of inner electrons
c) The distance of the electron from the nucleus
Chemical bonding

Chemical bonding are forces that hold atoms together to make compounds or molecules … the force
of attraction can be formed in different ways

 ionic bond: electrostatic attraction between positive and negative ions used to create an
ionic compound (total transfer of electrons). This attraction usually forms between a
metal and a non-metal.
 covalent bond: An interaction between two atoms, which involves the sharing of one
or more electrons to help each atom satisfy the octet rule. This interaction typically
forms between two non-metals.
 Metallic bonding is the main type of chemical bond that forms between metal atoms

Ionic Bonding
Ionic electrostatic attraction between positive and negative ions used to create an
ionic compound

 Generally occur between

1. Metal
2. Non metal

 Electrons are transferred from metals to non-metals

 Elements seeks to gain a full outer shell of electrons to be stable (noble
gas) chemically reaction allow the elements to obtain a full outer shells
What is an ionic lattice?

The ionic lattice is a giant structure of ions. The ions have a regular, repeating arrangement
called an ionic lattice.
The lattice is formed because the ions are attracted to each other and to other oppositely
charged ions in the sodium chloride compound by electrostatic force.

Physical properties

 They form crystals. ...

 They have high melting points and high boiling points. ...
 They're hard and brittle. ...
 They conduct electricity when they are dissolved in water but not in solid (because ions
are free to move in liquid state )
 Solid in room temperature
Covalent bonding
 Chemical bond that involves the sharing of electron pairs between atoms and the nuclei
of bonded atoms
 The electron pair is formed from an unpaired electron form each of the atoms
 This gives a region of negative charge between the two nuclei which attracts them and
holds them together.

 Usually occurs between two non-metals

 Draw dot and cross diagram showing 2 atoms of chlorine reaction

Covalent bonding can be represented by dot and cross diagrams showing the
electron pairing in the outer shells of the atoms. For HCl and NH3
Giant covalent structure

The are structures in which the atoms are linked in a three-dimensional network of covalent
bonds.

The atoms are usually arranged into giant regular lattices - extremely strong structures because of
the many bonds involved.

Physical properties (imp)

 They have high melting

 cannot conduct electricity or heat
 insoluble in all solvents
 Very hard but brittle

Graphite

 is a form of carbon in which the carbon atoms form layers

These layers can slide over each other, so graphite is much softer than diamond.

Diamond

1. The carbon atoms in diamond are held together by a network of strong covalent bonds
(very hard)
2. Silicon has the same structure but its bonds are longer and weaker so its less hard
Covalent Molecular Structures

 These are structures containing small molecules. The atoms within the molecules are
bonded by strong covalent bonds but the molecules are attracted to each other by weak
intermolecular forces

The Co-ordinate Bond (dative bond)

A co-ordinate bond is similar to the covalent bond in that it is a shared pair of electrons.
However, in a co-ordinate bond both electrons of the shared pair come from one of the
atoms.
 Compare between ionic and covalent bonding ?

Types of Structures
⚫ The structure of a substance is the way the particles (atoms, molecules or
ions) are arranged and how the attractive forces (bonds) between them
operate.
⚫ There are 4 main types of structure:
Shapes of Molecules
An atom in a molecules will be surrounded by a number of electron pairs.
These electron pairs will repel each other and get as far away from one another
as possible.
This determines the shape of the molecule
Polar molecules occur when there is an electronegativity difference between
the bonded atoms. Nonpolar molecules occur when electrons are shared equal
between atoms of a diatomic molecule or when polar bonds in a larger
molecule

A molecule is formed when two or more atoms join together chemically.

Diatomic molecules are made of two atoms of the same element.

Intermolecular forces are the attractive forces between molecules, between

ions, or between
ions and molecules.
• These are non-bonded interactions
• They don’t involve the transfer of any electrons
• They are result of the constant and random movement of electrons
within the shell of atoms

Question: What is the difference between Intramolecular and

Intermolecular Forces?
Intramolecular Force that hold atoms together in a molecule
Intermolecular are attractive forces between molecules

“Measure” of intermolecular force

• boiling point
• melting point

Factors that affects the strength of a dispersion force include: Distance

between molecules, polarizability and the shape of the molecule.
number of electrons increases, and so also does the radius of the atom. The
more electrons you have, and the more distance over which they can move, the
bigger the possible temporary dipoles and therefore the bigger the dispersion
forces

The noble gases and the alkanes all have low boiling points showing that the
intermolecular forces are very weak.

Their Boiling Points increase with Relative Molecular Mass showing the
intermolecular forces get stronger as the Relative Molecular Mass increases

In covalent molecular substances there are strong covalent bonds within the
molecules but much weaker forces of attraction between the molecules.
These weak forces of attraction are known as Intermolecular Forces.
The three main types of intermolecular force in order of strength are:

1. Induced Dipole Interactions (Van der Waals forces)

2. Permanent Dipole Interactions

3. Hydrogen Bonding

1. Induced Dipole Interactions

• In an atom, or molecule the motion of electrons is random so that at a

given instant there may be more electrons at one end of a molecule
than the other giving the molecule a slight polarity.
• This gives the molecule a transient dipole. At the next instant the
electrons may have moved and the dipole is reversed.
• All molecules possess this oscillating dipole and the dipole in one
molecule can induce dipoles in neighbouring molecules.
• Attraction between the positive and negative ends of these dipoles
gives a small attractive force.

Induced Dipole interactions are the only type of intermolecular force which
can exist between non-polar molecules and are very weak (very low
melting point and boiling point) . The strength of these forces increase
with relative atomic mass.

Permanent Dipole Interactions

• Molecules containing atoms with a significant difference in

electronegativity have a permanent dipole, e.g. HCl.
• An attraction can occur between the positive and negative ends of
these dipoles.
• This is a stronger attraction than induced dipole interactions.
Hydrogen Bonding

• In molecules which contain a hydrogen atom attached to a highly

electronegative atom (F, O, N) electrons are pulled away from the
hydrogen atom leaving it with a positive charge.
• Hydrogen Bonding in HF

• This positively charged hydrogen atom can then be attracted to a

negative lone pair in a neighbouring molecule.

• This attraction is called hydrogen bonding and is the strongest type of

intermolecular force.

Water is extensively hydrogen bonded which gives it some unusual

properties. Its melting and boiling points are much higher than would be
expected.

Boiling Points of Hydrides

NB The Boiling Points of H2O, HF and NH3 are anomalous in that they are
much higher than the other hydrides. They must have a much stronger
intermolecular force than Induced Dipole Interactions
Hydrogen Bonding in Water

In water each molecule can form 2 hydrogen bonds. These are formed by the
attraction of a +ve hydrogen atom to the -ve lone pairs on an oxygen atom in
a nearby molecule

Hydrogen Bonding in Ice

In ice the molecules have to move apart to allow a network of hydrogen

bonds to form. This makes ice less dense than water.

Anomalous Properties of Water

• Water has much higher melting and boiling points than would be
expected from its Relative Atomic Mass.
• The density of ice is less than that of water (molecules have to
move apart to allow a network of hydrogen bonds to form) so that
ice forms on the surface when water freezes.
Biological Importance of Hydrogen Bonding(DNA)

• Hydrogen bonding is extremely important in biological molecules.

• It holds protein molecules in a specific shape.
• It holds the base-pairs together in DNA.