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Topic A

Atomic Structure & Atomic Mass

❖ Protons, neutrons and electrons: locations, charges and masses. Positive
and negative ions.
❖ Mass number A and atomic number Z. Relative atomic mass (Ar).
❖ Calculation triangles (concentration, volume, no of moles, molar mass and
mass) and associated unit conversations.
❖ Definition of the term 'isotope'.
❖ Principles of the simple mass spectrometer to separate isotopes (include
diagram).
❖ Interpretation of simple elemental mass spectra, isotopic abundance and
atomic mass, mass-to-charge ratios. (This will include simple calculations.)

SLOs

A1 - Understand the structure of an atom in terms of protons, neutrons and

electrons
A2 – Understand the relative mass and charge of protons, neutrons and electrons.
A3 - Define the terms ‘mass number’ and ‘atomic number’, ‘relative atomic
mass’, ‘anion’ and ‘cation’.
A4 – Deduce the number of protons, neutrons and electrons in an atom or ion
given its mass number and atomic number.
A5 – Define the term ‘isotope’ and distinguish between isotopes of the same
element.
A6 – Describe and explain the functions of a simple mass spectrometer to
differentiate isotopes.
A7 – Describe how atomic masses and isotopic patterns are measured using the
mass spectrometer.
A8 – Calculate the relative atomic mass given the relative abundances of the
isotopes.
A9 – Calculate mass to charge ratios.
A10 – Analyse and predict mass spectrometry data and calculate relative atomic
masses.

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Structure of Atoms Atoms are made up of three particles. They are called
protons, neutrons and electrons.
Protons and neutrons have (almost) the same mass, but the mass of the electron is very small
compared with the other two particles.
 The mass of an electron is 1/ 1840 times the mass of a proton (it means an
electron is approximately 0.0005 times lighter than a proton).
• Each proton carries one unit positive charge (+1), same way each electron carries one
unit negative charge (−1). It means each electron carries equal and opposite charge to a
proton.
If there are 10 protons in an atom, then the total charge will be +10. Because the total
charge possessed by electrons is -10, the atom as a whole is neutral.
Neutrons do not carry any charge (0).
The atom has no overall charge; it is said to be electrically neutral.
 Each proton carries one unit mass (1), just as each neutron carries one unit mass,
exactly similar to a proton (1). The mass of an electron can be ignored since they are
very light particles.

Particle Relative electric Relative Mass

charge

Proton +1 1

Electron −1 approx. 1 /1840 of a proton

Neutron 0 1

Nucleus  Protons and neutrons make up the nucleus of an atom. The nucleus has a
positive charge because of the positively charged protons.
The electrons surrounded the nucleus in circular shells (or circular regions).
Because electrons are very light particles, the mass of an atom is due solely to its nucleus.

Electrons

+ Nucleus

(protons +neutrons)

Proton Number / Atomic Number  The number of protons in an atom is

called the proton number (also called the atomic number).

Every element has its own proton number.

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In the Periodic Table, elements are arranged in the increasing order of their proton number.
Atom is electrically neutral; therefore, the proton number is equal to the number of
electrons.

In an atom,

Proton number (atomic number) = Number of protons = Number of electrons

Nucleon Number / Mass Number 

It is the sum of the numbers of protons and neutrons in an atom. Each proton and neutron
carries 1 unit mass; therefore, the mass number of an atom will be the total number of
protons and neutrons present in the nucleus.
The mass of an atom is because of nucleus only, since electrons are very light particles.

Mass Number / Nucleon Number = Number of protons + Number of neutrons

Atomic mass (Relative Atomic Mass, Ar) is the actual mass of an isotope
expressed in atomic mass units (amu or simply u). It is to be noted that the masses of both
neutron and proton although very close, are not exactly equal to 1 amu. Hence, the atomic
mass can be fractional while the mass number is always a whole number.
The mass of an atom is very small. For example, the mass of a hydrogen atom is about 10 −24 g.
Since actual masses of atoms are so small; chemists do not use them in calculations. They only
need to compare the masses of different atoms.
They first started comparing the masses of different atoms with the mass of a hydrogen atom.
For example, one nitrogen atom is 14 times heavier than a hydrogen atom. Same way, an
oxygen atom is 16 times heavier than one hydrogen atom.
Therefore, we can say that the relative atomic mass of hydrogen is 14 and the relative atomic
mass of oxygen is 16.
Since it was not always convenient to compare the masses of different atoms with the mass of
a hydrogen atom. Therefore, in 1961 carbon - 12 (12C) was chosen as a new standard.
This is the isotope of carbon with a relative atomic mass of 12 means a carbon atom has 12
times the mass of one hydrogen atom. So, 1/12 th of a carbon atom has the same mass as one
hydrogen atom. Carbon consists of more than one isotope, so to be accurate, one particular
isotope 12C chosen for comparing the masses of atoms.
“The relative atomic mass of an element is the average mass of one atom of the element
when compared with 1/12 th of the mass of an atom”.

The relative atomic mass of an element is

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The average mass of one atom of the element

Ar = -----------------------------------------------------------------
The mass of 1/12 th of an atom of carbon-12

● The symbol for relative atomic mass is Ar

● The relative atomic mass has no units.

Relative Molecular Mass Like relative atomic mass, the relative molecular mass of
a molecule is

The average mass of one molecules of a substance

Mr = --------------------------------------------------------------------

The mass of 1/12 th of an atom of carbon-12

● The symbol for the relative molecular mass is Mr .

● The relative molecular mass is number with no units.
● The relative molecular mass of a molecule can be calculated by adding up relative atomic
masses of all atoms present in the molecule.

Atomic weight
The third term we need to know is atomic weight. It has its origin in the “relative natural
abundance” of isotopes. Since there is more than one isotope for any given element, it is
obvious that the total number of all the atoms of that particular element will have a certain
percentage of each of those. Let’s take the example of Chlorine. It has two stable isotopes
namely 35Cl and 37Cl. In the periodic table, however, the mass of a chlorine atom is given as
35.45 u. This results from the relative abundance of 75.76% of chlorine-35 and 24.24% of
chlorine-37.
Key Points:
1. Mass number = No. of neutrons + No. of protons
2. Atomic Mass = actual mass of an isotope expressed in amu.
3. Atomic Weight = Average of the masses of the stable isotopes of an element
according to their natural abundance.
NOTE:
 The number of neutrons in an atom is approximately the same as the number of protons,
up to 20 protons (i.e., up to proton number 20).
As the number of protons becomes larger, the number of neutrons becomes increasingly
greater than the number of protons. For example, an atom of lead has 82 protons but 125
neutrons.

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• It is important to note that in some cases the number of neutrons may be greater than by
one or two, but not by large numbers, which is why the word "approximately" is used.

For example, in fluorine (F), there are 9 protons, 9 electrons, and 10 neutrons.

Relative atomic mass (Ar) is the atomic weight compared to 1/12th mass of one atom
of carbon.

Symbolic Representation for the Structure of an Atom 

The mass number of an atom is usually written on the superscript of a symbol of an atom, and
the proton number is written in the subscript.

Mass
Number (A)

Symbol of an atom

Proton
Number (Z)

For example, the structure of some atoms in symbolic form is as follows:

Fluorine ( 169𝐹 ), Calcium ( 40
20𝐶𝑎 ), Chlorine ( 35 12
17𝐶𝑙 ), Carbon ( 6𝐶 ).

Cations and Anions 

In an ordinary atom, the number of protons equals the number of electrons, so the atom
normally has no electric charge one way or the other. An atom becomes negatively charged if
it gains extra electrons, and it becomes positively charged if it loses electrons. We use the
word "ion" to refer to atoms that have a charge one way or another, and we use the words
"cation" and "anion" to specify whether the charge is positive or negative.

A cation is formed when a metal atom loses an electron and changes into a positive ion. In
cation, electrons are less in number than protons, or there are more protons than electrons,
resulting in a positive charge.

M M+ + 𝑒 −

Example,

Li Li+ + 𝑒 −

In Lithium atom (Li), In Lithium ion (Li+),

No of protons = 3 No of protons = 3
No of electrons= 3 No of electrons= 2
Total charge = 0 ( +3 -3) Total charge = +1 ( +3 -2)

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Mg Mg2+ + 2𝑒 −

In Magneisum atom (Mg), In Magneisum ion (Mg2+),

No of protons = 12 No of protons = 12
No of electrons= 12 No of electrons= 10

Total charge = 0 ( +12 -12) Total charge = +2 ( +12 -10)

An anion is formed when a non-metal atom accepts an electron and changes into a negative
ion. In anion, electrons are more in number than protons, or there are less protons than
electrons, resulting in a negative charge.

X + 𝑒− 𝑋−

Example,

Cl + 𝑒 − 𝐶𝑙−

In Chlorine atom (Cl), In Chlorine ion (𝑪𝒍− ),

No of protons = 17 No of protons = 17
No of electrons= 17 No of electrons= 18
Total charge = 0 ( +17 -17) Total charge = -1 ( +17 -18)
O + 2𝑒 − 𝑂2−

In Oxygen atom (O), In Oxygen ion (𝑶𝟐− ),

No of protons = 8 No of protons = 8
No of electrons= 8 No of electrons= 10

Total charge = 0 ( +8 -8) Total charge = -2 ( +8 -10)

Electron Arrangement in Atoms / Electronic Structure Electrons in an atom move

around the nucleus in circular paths called shells. Each shell is numbered as 1, 2, 3, 4,…etc.,
or K, L, M, N..,etc., going outwards from the nucleus.
 Each can hold a certain maximum number of electrons given by 2n2 rule.
 The electrons and protons attract each other, but the net force is in the direction of the
nucleus because protons are heavier than neutrons. Therefore, we can say that an atomic
nucleus attracts electrons. This force of attraction is called electrostatic force. It is
important to note that this electrostatic force of attraction, called centrifugal force (toward
the nucleus), is exactly balanced by the centripetal force, just in the opposite direction but
equal in amount.
As a result, the electrons are not falling into the nucleus.

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Electrostatic force is balanced by

Centrifugal force

M
L
K
+ Maximum 2 electrons
1 2
3
Maximum 8 electrons

Maximum 8 electrons
upto proton no 20. Aftert that
maximum 18 electrons.

2n2 Rule → Before applying this rule, you must find out the proton number of an atom
or an element. Because an atom is neutral, this will tell you how many electrons are
present.
Now, based on the number of electrons, you can work out their arrangements.
According to this,
1. Filling of electrons always takes place from the shell nearest to the nucleus
i.e. 1st shell (K shell)
By keeping n = 1, (n refers shell number)
The first shell can accommodate the maximum number of electrons
= 2 (1)2 = 2
By keeping n = 2, (second shell)
The second shell can accommodate the maximum number of electrons
= 2 (2)2 = 8
By keeping n = 3, (third shell)
The third shell can accommodate the maximum number of electrons
= 2 (3)2 = 18
By keeping n = 4, (fourth shell)
The fourth shell can accommodate the maximum number of electrons
= 2 (4)2 = 32 and so on…
 Up to proton number 20 (Ca), the third shell also has the maximum capacity to
accommodate 8 electrons, not 18 electrons. (This is an exception to this rule)
Beyond proton number 20, the third shell a has a maximum capacity of
accommodating 18 electrons.
2. A shell can never have electrons more than its capacity. For example, the first shell can’t
take more than 2 electrons, the same way second shell cannot accommodate more than
8 electrons and so on.
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3. Each shell will always prefer to accommodate a maximum number of electrons (if that
much number of electrons are available) then the remaining electrons move to the next
shell.
For example, the electronic arrangement of sodium is as follows:
Na (proton no 11) = 11 electrons
Na = 2 ,8, 1
K = 2, 8, 8, 1
The electronic arrangements (electronic structures) can also be shown by showing the
electrons in the respective shells.

6+ 11+

Na(11) = 2, 8,1
C(6) = 2, 4

Electronic structure of sodium

Electronic structure of carbon

20+

Ca(20) = 2, 8, 8, 2
Electronic structure of calcium

Valence shell (Outer shell) The shell which is furthest from the nucleus is called the
outer shell. It is also called a valence shell.
 The electrons present in the valence shell are called valence electrons or outer
electrons.
 In all chemical reactions only valence electrons are involved in the reactions.
 Sometimes only outer electronic structures are drawn.

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The outer electronic structure of sulphur and nitrogen is shown below.

S
N

S(16) = 2, 8, 6 N(7 ) = 2, 5

Outer electronic structure of sulphur Outer electronic structure of Nitrogen

Isotopes
Generally, most of the atoms of an element are similar in all respects, i.e., they have the same
mass number and proton number, but in some cases (the atoms of some elements), not all the
atoms of an element are the same. For example, most carbon atoms contain 6 neutrons
( 126𝐶 ), but some have 7 neutrons, and a few have 8 neutrons. These different carbon atoms are
called isotopes.

It is defined as follows:
“Isotopes are the atoms of the same element with the same proton number but different
mass number.”
or
“Isotopes are atoms of the same element with different number of neutrons.”

The isotopes of some elements are as follows:

❖ There are three isotopes of carbon:

1
1H ( called Protium), 1H2 ( called Deuterium ) and 1H3 ( called Tritium )

1p 1p 1p
1n 2n

1 2 3
1𝐻 1𝐻 or 1D2 1𝐻 or 1T3
The relative occurrence of 11𝐻 in hydrogen is 99.985% [Non radioactive]
The relative occurrence of 21𝐻(1D2) in hydrogen is 0.015% [Non radioactive]
The relative occurrence of 31𝐻 (1T 3) in hydrogen is 10−15 % [Radioactive]

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3
1H is prepared artificially by the bombardment of nitrogen or an isotope of lithium with
neutrons.
14
7𝑁 + 0n 1 ⎯→ 12
6𝐶 + 1 H
3

6
3𝐿𝑖 + 0n 1 ⎯→ 4
2𝐻𝑒 + 3
1𝐻

Tritium being unstable because of its radioactive nature occurs only in traces (one in
1017 parts)

❖ There are three naturally occurring isotopes of oxygen:

16 17
8 O , 8O and 8O18

16 16
16
8p 8p
8n 9n 8p
10n

The relative occurrence of 8O16 in oxygen is 99.76% [Non radioactive]

The relative occurrence of 8O17 in oxygen is 0.037% [Non radioactive]
The relative occurrence of 8O18 in oxygen is 0.204% [Radioactive]
The radioactive isotope of oxygen, 8O18 is widely used in studying the mechanism of
organic reactions and in other tracer techniques.

❖ There are three naturally occurring isotopes of carbon

12
6C , 6C13 and 6C14
14
6C isotope of carbon is radioactive. This isotope is used in radio carbon dating (in
predicting the age of fallen tree or dead animal)

Characteristics of Isotopes
1. Isotopes of the same element have the same chemical properties and form compounds
with the same chemical formula.
2. Isotopes have small differences in physical properties like boiling points, density,
surface tension, etc.
3. Isotopes can be divided into two types, i.e., radioactive and non-radioactive isotopes.

Radioactive Isotopes Radioactive isotopes give out radiation. This radiation is invisible but
it can be detected with special instruments. Radiation is harmful to life, and a large amount
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can kill people. Workers handling radioactive isotopes must take precautions to shield
themselves from radiation.
Example,
3
1H (1T 3) or Tritium , 8O18 , 6C14 , , 27Co
60
,

 Most isotopes in the air and the ground are non-radioactive and they do not produce
radiation.
 Most radioactive isotopes are made artificially.

Important uses of Radioactive Isotopes Radioactive isotopes have important uses. The
uses of some radioactive isotopes are as follows:
1. The cobalt isotope, Co60, is used in hospitals to treat cancer patients. The intense
radiation from this isotope destroys the cancer cells.
Co60 is also used to sterilize surgical instruments used in hospital operations. The
powerful radiation kills germs.
2. The radioactive isotope, 94Pu 239 (artificially prepared ) is used in making atom bombs
and nuclear reactors because it undergoes chain reactions much more easily similar to
the naturally occurring uranium, U235.

92U
238
+ 0n
1
→ 92U
239
→ 93Np
239
+ −1e
0

unstable Neptunium electron

(-particle)

93Np
239
⎯⎯→ 94Pu
239
+ − 1e
0

Plutonium electron
(-particle)
This radioactive isotope, 92Pu239 is also used (in small amounts) in pacemakers. A
pacemaker is an instrument that provides a tiny electrical shock to regulate the
heartbeat. This is needed by people who have irregular heartbeats.
The advantage of powering a pacemaker with a radioactive isotope is that it can work
reliably for over 20 years while an ordinary battery would have to be replaced every 10
years.
3. The radioactive isotope of iodine, 53I131, is used for the treatment of thyroid disorders.
4. The amount of uptake of a phosphate fertilizer by different parts of the plants can be
easily studied by using a fertilizer containing a radioactive isotope of phosphorous, 15P32.
5. By injecting a saline solution containing a little, Na24, the circulation of blood can be
followed.
6. Apart from the above uses radioactive isotopes can be used to produce electrical energy
by controlled chain reaction carried out in a nuclear reactor.
Small amounts of radioactive isotopes is used to supply energy in remote places.
7. Radioactive isotopes provide energy for spacecraft exploring the outer planets.

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Counting Atoms & Molecules Matter is made of tiny particles called

atoms or molecules. Even a single drop of water contains about 2000 trillion molecules and 1-
cm length of magnesium ribbon contains around 5000 trillion atoms.
Chemists measure amounts of particles such as atoms, ions and molecules used in calculations
in moles. This is due to the reason that atoms and molecules are so small in size that it is not
possible to count them individually. Moreover, the smallest sample of the substance that we
may take contains a very large number of atoms or molecules. Therefore, in order to
overcome these difficulties, the concept of the mole was introduced.
According to this concept number of particles of the substance is related to the mass of the
substance.
For this number of atoms in 12g of carbon-12 isotope is taken as standard.
This number has been experimentally found to be 6.023  1023 and is called one mole.
This number is also known as Avogadro’s number or Avogadro’s constant (NO).
One mole of matter contains about 6.023  1023 particles.
So, one mole of magnesium metal contains about 6.023  1023 atoms and two moles of
magnesium metal contains 2 6.023  1023 atoms.
NOTE:
• The symbol for mole is mol. It is a number with no units.
• The mole may be defined as the amount of the substances that contains as many as
specified elementary particles as the number of atoms in 12 g of C-12 isotope.
These elementary particles may be atoms, molecules or any discrete particles such as ions,
electrons etc.

Moles of Atoms The mass of one mole of any substance is called molar mass.
For atoms of elements, the molar mass is the relative atomic mass of the elements expressed
in grams.
The molar mass of an element is the relative atomic mass in grams.
For example, the relative atomic mass of carbon is 12. So, the molar mass of carbon (atoms) is
12 grams because 12 grams of carbon contains 1 mole of atoms.
Using molar mass, we can easily calculate the number of moles of atoms in a known sample of
the element.

Mass of the sample in grams

Number of moles of atoms = -------------------------------------
in a sample of an element Molar mass of the element

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The molar mass of any element contains 1 mole of atoms. This is shown in the table.
Same way, the molar mass of any compound contains 1 mole of molecules.

Concentration of Solution When a substance is dissolved in a solvent, a

solution is produced.
The volume of a solution is usually measured in cm3 or dm3, where
1 dm3 = 1000 cm3 = 1 litre

The concentration of a solution tells you the amount of solute in 1dm3 of solution.
● Concentrations are measured in grams per dm3 (g/dm3) or in moles per dm3 (mol/dm3)
● Concentrations are measured in grams per dm3 (g/dm3) is called Normality.
(Expressed in N) while concentrations are measured in moles per dm3 (mol/dm3) is known
as Molarity (Expressed as M)
● 1 M solution (one molar solution) is the solution in which 1 mole of solute is present in
1dm3 of solution.
1 N solution (one normal solution) is the solution in which 1 gram-equivalent of solute is
present in 1dm3 of solution.
For example, a concentration of 10.0 g/dm3 means that there are 10.0 g of solute in every
dm3 of solution.
Concentrations in g/dm3 can be changed into concentrations in mol/dm3 using following
relationship.

Concentration in g/dm3
Concentration in mol/dm3 = ----------------------------------
Molar mass of the solute

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Mass Spectrometry
Herein comes the importance of isotopes – two or more forms of the same element having
different numbers of neutrons. What it means is that the mass of an isotope differs from that
of another isotope of the same element. This difference in isotopes is very useful in analysis
using mass spectrometry. Mass Spectrometry is founded on the principle of separation of the
charged particles in a vacuum through the force exerted by the magnetic and electric fields.
This separation is a result of the mass-to-charge ratio (m/z) of individual ionic fragments.
Often, the ions produced during mass spectrometry are singly charged (z=1), which effectively
shortens the mass-to-charge ratio to the more easily calculated term mass. Before going
further into the intricacies of understanding the output from a mass spectrometer, we should
have a clear understanding of the terms mass number, atomic mass, and atomic weight.

Key Points:
1. Atom is the most fundamental particle in chemical reactions.
2. Chemical reactions are influenced by a number of protons and electrons, but only
negligibly by the number of neutrons.
3. Neutrons are the distinguishing factor in isotopes and this is useful in analyzing
chemical composition by mass spectrometry.

Principles of the Simple Mass Spectrometer

In 1919, Aston invented the mass spectrometer, using which selective masses of atoms could
be compared with accuracy.
Basic idea of mass spectrometer can be explained by using the apparatus in which the wooden
balls of different sizes but with identical iron cores roll down a sloping plane.
At the bottom of the slope, a powerful magnet attracts the iron cores, as a result of the
moving balls are deflected.
Since the balls have identical iron cores, they are all attracted equally by magnet. But the
smaller balls are lighter and therefore they are deflected most. The balls collect in different
compartments depending on their mass. All balls of the same mass collect in the same
compartment. Using this simple apparatus, it is possible to separate the different sized balls
according to their mass and to find the relative numbers of each present.

A simple model to illustrate the working of a mass spectrometer

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This describes how a mass spectrum is produced using a mass spectrometer.

A real mass spectrometer works in a similar fashion to this simple model. It separates the
atoms according to their mass and shows the relative numbers of different atoms present.
Before the atoms can be deflected and separated, they must be converted to positively
charged ions.
In a mass spectrometer, there are five main stages:-

1. Vaporisation
2 Ionisation
3. Acceleration
4. Deflection
5. Detection

1. Vaporisation Gases, liquids, and volatile solids are injected into the instrument just
before the ionization chamber.

2. Ionisation The atom is ionised by knocking one or more electrons off to give a positive
ion. This is true even for things that you would normally expect to form
negative ions (chlorine, for example) or never form ions at all (argon, for
example). Mass spectrometers always work with positive ions.
After vaporization, the element passes into the ionization chamber.
In an ionization chamber, atoms of the element are bombarded with a
stream of high- energy electrons. This causes ionization.

𝑒− + X → X+ + 𝑒− + 𝑒−
↓
electron
knocked out

𝑒− + X → X++ + 𝑒− + 𝑒− + 𝑒−

electrons
knocked out

3. Acceleration The ions are accelerated so that they all have the same kinetic energy.
These positive ions now pass through holes in the parallel plate to which an
electric field is applied. The electric field accelerates the ions into the
instrument towards the magnetic field.

4. Deflection The ions are then deflected by a magnetic field according to their masses.
The lighter they are, the more they are deflected.

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The amount of deflection also depends on the number of positive charges

on the ion - in other words, on how many electrons were knocked off in the
first stage. The more the ion is charged, the more it gets deflected.

As the ions pass through the magnetic field, they are deflected according to
their mass and charge.
That particle can only pass through the instrument if they are positively
charged.

5. Detection The beam of ions passing through the machine is detected electrically. If
the accelerating electric field and magnetic field stay constant, ions of
only one particular mass/charge (m/z)ratio will hit the ion detector at end
of the apparatus.

Ions of a smaller mass/charge ratio (m/z) will be deflected too much. Ions
of greater mass/charge ratio will be deflected too little.
The ion detector is usually linked to an amplifier to a recorder.

A full diagram of a mass spectrometer

As the strength of the magnetic field is slowly increased, ions of increasing mass will be
detected and the mass spectrum similar to that shown is obtained.

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( relativeAbundance )
Detector current or

Relative atomic mass

The relative heights of the peak in the mass spectrum give a measure of the relative amounts
of different ions present (It is in fact area under the peak, not peak heights).
In practice, the peak of a known substance is first obtained on the mass spectrum. The relative
masses of other particles can then be obtained by comparison with this.

Understanding what's going on…..

The need for a vacuum

It's important that the ions produced in the ionisation chamber have a free run through the
machine without hitting air molecules.

Ionisation

The vaporised sample passes into the ionisation chamber. The electrically heated metal coil
gives off electrons which are attracted to the electron trap which is a positively charged plate.

The particles in the sample (atoms or molecules) are therefore bombarded with a stream of
electrons, and some of the collisions are energetic enough to knock one or more electrons out
of the sample particles to make positive ions.

Most of the positive ions formed will carry a charge of +1 because it is much more difficult to
remove further electrons from an already positive ion.

These positive ions are persuaded out into the rest of the machine by the ion repeller which is
another metal plate carrying a slight positive charge.

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Note: As you will see in a moment, the whole ionisation chamber is held at a positive voltage
of about 10,000 volts. The two plates having positive charges, these charges are in
addition to that of 10,000 volts.

Acceleration

The positive ions are repelled away from the very positive ionisation chamber and pass
through three slits, the final one of which is at zero(0) volts. The middle slit carries some
intermediate voltage. All the ions are all accelerated into a finely focused beam.

Deflection

Different ions are deflected by the magnetic field by different amounts. The amount of
deflection depends on:

• the mass of the ion. Lighter ions are deflected more than heavier ones.
• the charge on the ion. Ions with 2 (or more) positive charges are deflected more than
ones with only 1 positive charge.

These two factors are combined into the mass/charge ratio. Mass/charge ratio is given the
symbol m/z (or sometimes m/e).

For example, if an ion had a mass of 28 and a charge of 1+, its mass/charge ratio would be 28.
An ion with a mass of 56 and a charge of 2+ would also have a mass/charge ratio of 28.

In the following diagram, ion stream A is most deflected - it will contain ions with the smallest
mass/charge ratio. Ion stream C is the least deflected - it contains ions with the greatest
mass/charge ratio.

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It makes it simpler to talk about this if we assume that the charge on all the ions is 1+. Most of
the ions passing through the mass spectrometer will have a charge of 1+, so that the
mass/charge ratio will be the same as the mass of the ion.

Assuming 1+ ions, stream A has the lightest ions, stream B the next lightest and stream C the
heaviest. Lighter ions are going to be more deflected than heavy ones.

Detection

Only ion stream B makes it right through the machine to the ion detector. The other ions
collide with the walls, where they will pick up electrons and be neutralised. Eventually, they
get removed from the mass spectrometer by the vacuum pump.

When an ion hits the metal box, its charge is neutralised by an electron jumping from the
metal on to the ion (right hand diagram). That leaves a space amongst the electrons in the
metal, and the electrons in the wire shuffle along to fill it.

A flow of electrons in the wire is detected as an electric current which can be amplified and
recorded. The more ions arriving, the greater the current.

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Detecting the other ions

How might the other ions be detected - those in streams A and C that have been lost in the
machine?

Remember that stream A was most deflected - it has the smallest value of m/z (the lightest
ions if the charge is 1+). To bring them on to the detector, you would need to deflect them
less, by using a smaller magnetic field (a smaller sideways force).

To bring those with a larger m/z value (the heavier ions if the charge is +1) on to the detector
you would have to deflect them more by using a larger magnetic field.

If you vary the magnetic field, you can bring each ion stream in turn on to the detector to
produce a current which is proportional to the number of ions arriving. The mass of each ion
being detected is related to the size of the magnetic field used to bring it on to the detector.
The machine can be calibrated to record current (which is a measure of the number of ions)
against m/z directly. The mass is measured on the 12C scale.

What the mass spectrometer output looks like

The output from the chart recorder is usually simplified into a "stick diagram". This shows the
relative current produced by ions of varying mass/charge ratio.

The stick diagram for molybdenum looks like this:

You may find diagrams in which the vertical axis is labelled as either "relative abundance" or
"relative intensity". Whichever is used, it means the same thing. The vertical scale is related to
the current received by the chart recorder - and so to the number of ions arriving at the
detector: the greater the current, the more abundant the ion.

As you will see from the diagram, the commonest ion has a mass/charge ratio of 98. Other
ions have mass/charge ratios of 92, 94, 95, 96, 97 and 100.

That means that molybdenum consists of 7 different isotopes. Assuming that the ions all have
a charge of 1+, that means that the masses of the 7 isotopes on the carbon-12 scale are 92, 94,
95, 96, 97, 98 and 100.

Note: If there were also 2+ ions present, you would know because every one of the lines in the stick diagram would have another
line at exactly half its m/z value (because, for example, 98/2 = 49). Those lines would be much less tall than the 1+ ion
lines because the chances of forming 2+ ions are much less than forming 1+ ions.

NOTE : Knowledge of the working of the mass spectrometer is not

required as per your syllabus.
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Isotopes and Mass Spectrometry

The technique of mass spectrometry can distinguish these two isotopes of chlorine, and
similarly, any number of isotopes an element may have. The output is presented in an x-y plot
where the x-axis represents the mass-to-charge ratio and the y-axis represents the relative
abundance. When applied to a sample of a pure element, mass spectrometry reveals each
isotope as a separate peak. This technique can be used not only for identifying the relative
abundance of isotopes in a sample of an element, but also to identify the presence and
percentage of each element in a compound. Since the relative abundance of isotopes is used
in this technique, the y-axis does not have any unit, and hence, the highest among the peaks
obtained in a mass spectrum is assigned as the “base peak” and taken as 100% (not to be
confused with the total abundance of each element). All the other peaks are assigned as a
percentage of the base peak.

To identify the isotopes and their contributions in a mass spectrum of a compound, the following
terms need to be highlighted:

1. Exact mass – It is the calculated mass obtained by summation of masses of

individual isotopes. If an exact mass is presented without mentioning the
isotope, it is generally considered to have been calculated with the mass of the
most abundant isotopic species.
2. Molecular weight – It is the summation of atomic weights of the elements
present in a compound.
3. Accurate mass – Defined by IUPAC as “Experimentally determined mass of anion
of known charge”. This is used to determine the composition of elements in a
compound. This is the mass obtained from the m/z ratio.
Key Points:
1. Mass spectrum is obtained as an x-y plot where the x-axis represents the mass-
to-charge ratio and the y-axis represents the relative abundance.
2. The highest peak is taken as the “base peak” (100%) and all other peaks are
assigned as a percentage of that.
3. Exact Mass = summation of masses of individual isotopes.
4. Molecular weight = summation of atomic weights of the elements present in a
compound.
5. Accurate mass = Experimentally determined mass of anion of known charge

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Analyzing Atoms and Molecules

A. Mass Spectrum of Monatomic Elements
Monatomic elements contain only one atom, except for things like chlorine, Cl 2, which has
molecules containing more than one atom.

A simple element passed through a mass spectrometer will generate a single peak.

1. The mass spectrum for Sodium (Na)

Sodium, for example, will generate the response illustrated below:

100%
Abundance

50%

0%
23
Relative Isotopic Mass

Mass spectrum of sodium

The relative atomic mass is determined with the relative abundance set at 100%, as no
other species are present.

2. The mass spectrum for boron (B)

Relative Isotopic Mass

The number of isotopes →

The two peaks in the mass spectrum shows that there are 2 isotopes of boron - with
relative isotopic masses of 10 and 11 on the 12C scale.

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The abundance of the isotopes →

The relative sizes of the peaks give you a direct measure of the relative abundances of the
isotopes. The tallest peak is often given an arbitrary height of 100, but you may find all
sorts of other scales used. It doesn't matter in the least.
You can find the relative abundances by measuring the lines on the stick diagram.
In this case, the two isotopes (with their relative abundances) are:
boron-10 23
boron-11 100

Working out the relative atomic mass →

The relative atomic mass (RAM) of an element is given the symbol Ar and is defined as:

The relative atomic mass of an element is the weighted average of the masses of the
isotopes relative to 1/12 of the mass of a carbon-12 atom.

A "weighted average" allows for the fact that there won't be equal amounts of the various
isotopes.

Suppose you had 123 typical atoms of boron. 23 of these would be 10B and 100 would
be 11B.
The total mass of these would be (23 x 10) + (100 x 11) = 1330

The average mass of these 123 atoms would be 1330 / 123 = 10.8 (to 3 significant figures).
10.8 is the relative atomic mass of boron.

Notice the effect of the "weighted" average. A simple average of 10 and 11 is, of course,
10.5. Our answer of 10.8 allows for the fact that there are a lot more of the heavier
isotope of boron - and so the "weighted" average ought to be closer to that.

3. The mass spectrum for zirconium (Zr)

Relative Isotopic Mass

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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 →

This time, 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

Note:
You almost certainly wouldn't be able to measure these peaks with this degree of
accuracy, but in exams, examiners may well give you the data in number form anyway.
We'll do the sum with the more accurate figures.

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.

The total mass of these 100 typical atoms would be

(51.5 x 90) + (11.2 x 91) + (17.1 x 92) + (17.4 x 94) + (2.8 x 96) = 9131.8

The average mass of these 100 atoms would be 9131.8 / 100 = 91.3 (to 3 significant
figures).

91.3 is the relative atomic mass of zirconium (Zr).

B. Mass Spectrum of Diatomic Elements

1. The mass spectrum for Chlorine (Cl)

Chlorine is taken as typical of elements with more than one atom per molecule. We'll look
at its mass spectrum to show the sort of problems involved.

Detecting Isotopes→ Mass spectrometry can be utilized to analyze atomic species that
exist as a number of isotopes. Chlorine exists naturally in two forms 35Cl and 37Cl, with a
ratio of 3:1.
The spectrum below shows the response generated by a natural sample of chlorine.
You might suppose that the mass spectrum would look like this:

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or

100%

75% Abundant
Abundance

50%

25% Abundant

0%
35 37
Mass
35Cl 37Cl
Mass spectrum of (75%) & (25%)

You would be wrong!

The problem is that chlorine consists of molecules, not individual atoms. When chlorine is
passed into the ionisation chamber, an electron is knocked off the molecule to give a
molecular ion, Cl2+. These ions won't be particularly stable, and some will fall apart to give a
chlorine atom and a Cl+ ion. The term for this is fragmentation.

Cl2+ Cl + Cl+

If the Cl atom formed isn't then ionised in the ionisation chamber, it simply gets lost in the
machine - neither accelerated nor deflected.

The Cl+ ions will pass through the machine and will give lines at 35 and 37, depending on
the isotope and you would get exactly the pattern in the last diagram. The problem is that
you will also record lines for the unfragmented Cl2+ ions.

Think about the possible combinations of chlorine-35 and chlorine-37 atoms in a Cl2+ ion.

Both atoms could be 35Cl, both atoms could be 37Cl, or you could have one of each sort.
That would give you total masses of the Cl2+ ion of:

35 + 35 = 70
35 + 37 = 72
37 + 37 = 74

That means that you would get a set of lines in the m/z = 70 region looking like this:

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Abundance

Relative Isotopic Mass

Analyzing Compounds
Fragmentation
The ionization process used by a mass spectrometer will tend to cause fragmentation of
compounds. This will generate a number of different species, with some traces becoming very
complex.
The M+ may collide with a second electron to form two lighter fragments. If, in addition, the
compound contains an isotope, the trace will become yet more complicated. These factors
must be taken into account when analyzing mass spectra.
Many pain killing medicines rely on active ingredient Salicylic acid, more commonly known as
Aspirin. This compound can be analyzed using mass spectrometry to elucidate structure.

1 COOH
2
OH

2- Hydroxybenzoic acid
(Salicyclic acid)

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The corresponding mass spectrum appears below:

Base peak (92)

100%

Molecular ion (138)

Abundance

50%

25% Abundant

0%
40 60 80 10 120 14

Mass

Firstly, we should note the heaviest ion present, which corresponds to the compound with
one electron missing. It registers at 138 and it is known as molecular ion.
We therefore, know the mass of the salicylic acid. The most abundant species is known as
the base peak. In the previous spectrum it has a weight of 92 units and is assigned a relative
intensity of 100%.
The modern databases allow a mass spectroscopist to cross – reference his data with
previously recorded and archived data. This will not always yield a direct answer but will
require further assessment often requiring the use of the other analytical techniques.

The molecular ion, as previously observed, has a weight of 138 units and an empirical
formula of C7H6O3. But it could theoretically have more than one structure.
By studying this structure (of salicylic acid) and others suggested by experiment along with
the fragments that are presented in the mass spectrum. It can only be determined that only
this spectrum can be correct.

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