Atomic Structure

Protons and Neutrons

In an atom there is a nucleus, which is tiny but massive; the majority of mass is
concentrated here. The nucleus contains protons and neutrons which both have
a relative mass of 1. Protons have a relative charge of +1 and neutrons have no
charge. The number of protons in an atom is equal to the number of electrons in
an atom; an ion is a charged atom due to a difference in the number of protons
and neutrons. The proton number/atomic number defines the element. The
mass number of an element is the average relative atomic mass of an atom of
that element, taking into account naturally occurring isotopes. An isotope of an
element is any element that can have two of more values for the number of
neutrons.
Electron Configuration
Electrons have a relative charge of -1 and a relatively negligible mass. They are
located on energy levels surrounding the nucleus. Energy levels fill up from
closest to the nucleus outwards, and can hold increasing numbers of electrons in
the form [2,8,8,18]. This is why periods in the periodic table are arranged to hold
[2,8,8,18] elements moving down the table. The groups in the periodic table are
arranged by the number of electrons an element has on the outer shell.
Each energy level (1, 2, 3, 4) is split into sub-levels (s, p and d). Each s level can
hold 1 pair of electrons, p can hold 3 pairs and d can hold 5 pairs. Electrons
always fill up an empty sub-level before moving onto the next one. Electrons
repel so they occupy empty spaces on the sub-level before being paired up.
Pairs of electrons are represented by to show electrons spinning in opposite
directions to minimise repulsion. The levels are:
1s2, 2s2, 2p6, 3s2, 3p6, 4s2, 3d10, 4p6
There are two exceptions to the rules on electron configuration. Copper and
Chromium have alternative arrangements.
Chromium: 1s2, 2s2, 2p6, 3s2, 3p6, 4s1, 3d5
As the 4s and 3d levels are very close in terms of energy the second 4s electrons
moves to the 3d level to avoid being paired.
Copper: 1s2, 2s2, 2p6, 3s2, 3p6, 4s1, 3d10
As the 4s and 3d levels are very close in terms of energy the second 4s electron
moves to the 3d level to make a full d shell, making the atom more stable.
When negative ions are formed, electrons are added in the same way as they
would as proton number increase. When positive ions are formed the highest
energy level electrons are removed, paired electrons first. However 4s electrons
are removed before 3d electrons.

First Ionisation Energy

Definition of first ionisation energy:
The energy required to remove one mole of electrons from one mole of gaseous
atoms
Equation of first ionisation energy:
X(g) X+(g) + eThe first ionisation energy generally increases across a period. This is because
moving across a period there is a greater nuclear charge, but there is negligible
increase in shielding, so electrostatic attraction to the outer electron increases
therefore more energy is required to remove this electron. The higher an
element is in its group the higher the first ionisation energy, because there are
less electron shells between the outer electron and the nucleus, so less shielding
occurs. In elements lower down the group, shielding overcomes the extra
attraction from the increased nuclear charge, meaning that less energy is
required to remove the outer electron from elements lower in the group.
Group 3 first ionisation level is lower than the general trend. This is because
their outer electron is the first on a higher energy level. This means the distance
from the nucleus to the outer electron increases and less energy is required to
remove this electron.
Group 6 first ionisation level is also lower than the general trend. This is because
their outer electron forms the first pair of electrons on the p shell. As electrons
repel, this electron requires less energy to remove it.
The Mass Spectrometer
The mass spectrometer is used to identify elements and compound according to
their mass/charge ratio.
1. The sample to be investigated is vaporised, giving the sample more energy
2. An electron gun then fires high energy electrons at the sample.
3. The electrons knock off electrons from the sample to form positive ions, so that
the sample can be accelerated, deflected and detected.
4. The ions are accelerated into a single beam by an electrically charged plate.
5. An electromagnetic field strength is varied to ensure all ions are deflected into
the detector
6. Lighter, more highly charged ions are deflected more.

7. As ions hit the metal in the detector they gain an electron, becoming atoms.
There is then an electron missing from the metal so other electrons move the fill
this space creating a tiny magnetic current, which is then amplified and
recorded.
8. The more ions collected at specific magnetic field strength the greater the
current.
A vacuum pump in used in the mass spectrometer to stop molecules in air from
knocking the ions off course. Practical uses of the mass spectrometer include
drugs testing, testing for pesticides and carbon dating used for forensics and
archaeology.
To find the relative atomic mass of an element from a mass spectrum graph,
multiply the heights of each peak by the m/z ratio of each peak, and divide by
the sum of the m/z ratio. The relative formula mass of a compound is the highest
peak on the right hand side of a mass spectrum graph. Anomalies occur in mass
spectrum graphs because of isotopes, the formation of 2+ ions, halving the m/z
ratio, and high speed electrons breaking compounds into two.

Bonding
Electro negativity
Electro negativity is a measurement of the power of an atom to attract electron
density in a covalent bond towards itself.
Highly electro negative atoms are likely to form negative ions. Electro negativity
decreases down a period because the nuclear attraction to the electron density
is shielded by more inner electron levels and there is less electrostatic attraction
to the nucleus. Electro negativity increases across the period because there is
no increase is shielding and the nuclear charge increases, increasing
electrostatic attraction to the electron density. Group 8 elements dont have a
value for electro negativity because they have a full outer shell and therefore
dont form bonds.
A pure covalent bond can only be formed between two atoms of the same
element because they both attract the electron density equally. The greater the
difference in electro negativity between two or more atoms, the more polar a
covalent bond becomes, meaning that one atom attracts the electron density
towards itself more than the other(s).
Intermolecular Forces

Van Der Waals Forces

Weak forces of attraction between all molecules. The bigger the molecule the
stronger the Van Der Waals forces.

Dipole-Dipole Interaction

Weak forces of attraction between polar molecules. The more polar a molecule
the stronger the dipole-dipole attraction.

Hydrogen Bonds

Relatively strong forces of attraction between molecules containing hydrogen

and highly electronegative elements Nitrogen, Oxygen and Fluorine.

Magnesium (Mg)
Magnesium is a metal with 2 electrons on the
outer shell. In metallic bonding outer electrons
become delocalised and form a sea of electrons
around the positive metal ions. The ions and free
electrons form an ionic lattice, held together by
strong electrostatic attraction giving magnesium
a high melting point. Magnesium is malleable
and ductile, because the ions can slide over each other but are still held in
together by electrostatic attraction. These electrons can move within
Magnesium carrying an electrical charge, and therefore magnesium conduct
electricity. Free electrons also cause magnesium to be shiny.
Graphite (C)
Graphite is an allotrope of carbon, with each atom
forming 3 pure covalent bonds in macromolecular
layers. One electron from each atom then becomes
delocalised forming a sea of electrons between layers.
Graphite is relatively soft because the layers are held
together by weak electrostatic attraction and Van Der
Waals forces, so are able to slide over one another.
The free electrons between layers can move causing
graphite to conduct an electrical current.
Diamond (C)
Diamond is an allotrope of carbon, with each atom forming four pure covalent
bonds in a macromolecular lattice structure. Diamond has a very high melting
point because to melt it a lot of energy is needed to overcome the many strong
covalent bonds. The structure of diamond is tetrahedral the bond angles are
109.5, the largest possible angle for a 3D structure, making it one of the hardest
known substances.

Silicon Dioxide (SiO2)

In silicon dioxide, each silicon
atom forms four covalent
bonds with oxygen atoms and
each oxygen two covalent
bonds with silicon in a
macromolecular structure. The
structure of silicon dioxide is
tetrahedral the bond angles
are 109.5, the largest
possible angle for a 3D
structure, making it one of the hardest known substances. Silicon dioxide has a
very high melting point because to melt it a lot of energy is needed to overcome
the covalent bonds.
Iodine (I2)
Iodine is a diatomic molecule. Each atom forms a single pure
covalent bond with another iodine atom to fill the outer electron
shell and make each atom more stable. Iodine has a high
proton number, and therefore a high number of electrons. The
Van der Waals forces between each molecule are therefore
very strong and a lot of energy is required to overcome these
forces and melt iodine.
Sodium Chloride (NaCl)
Each sodium atom looses one electron to a chlorine
atom, forming a +1 sodium ion and a -1 chlorine ion, in
a highly ionic compound. The ions are arranged in an
ionic lattice, held together by strong electrostatic
attraction between positive and negative ions. Sodium
chloride has a high melting point because a lot of
energy is required to overcome the electrostatic
attraction. The charged particles in sodium chloride are
able to conduct an electrical current when they are
molten or in solution.
Ice (H2O)
In H2O, an oxygen atom forms two covalent bonds with two hydrogen atoms,
leaving the oxygen atom with two lone pairs of electrons. In ice, both these lone
pairs form hydrogen bonds with hydrogen atoms from other molecules. Each
molecule therefore has four hydrogen bonds and together they form a
tetrahedral structure, with bond angles (hydrogen and covalent) of 109.5, the
maximum angle for a 3D structure, so ice is very hard. Ice has a higher melting

point than normal for such a small molecule, because

of the extra energy required to break the hydrogen
bonds between the molecules.
Change of State Graph
The graph shows
a substance
cooling from a
gas to a solid. At first
the temperature
drops over time, but
then the
temperature remains
the same. This
is due to bonds being
made as the
substance changes
from a gas to a
liquid. Bonds being
made release
energy at the same
rate that energy
is dispersing to the environment, so the temperature remains the same until the
substance has become a liquid and all the bonds are made and no more energy
is released.
Valence Electron Shell Repulsion Theory
The shape of a molecule is determined by the number of bonding and nonbonding pairs on the central atom. Electron pairs repel one another, and nonbonding pairs repel more than bonding pairs. The shapes of molecules are
drawn with dashed lines representing bonds that go behind the shape and
triangles representing bonds that come in front of the shape.
Molecule
Bonding
Diagram

Non-Bonding

Shape

Bond angles

Methane
CH4

Tetrahedral 109.5

Ammonia
NH3

Trigonal
Pyramidal

107

Water
H 2O

V shaped
or Bent

104.5

Boron
Trifluoride
BCl3

Trigonal
Planar

120

Phosphorus 5
V Chloride
PCl5

Trigonal
90 and 120
Bipyramidal

Sulphur
6
Hexafluoride
SF6

Octahedral

90

Coordinate Bonding
A coordinate bond is a covalent bond, however unlike a simple covalent bond
where each atom supplies one electron, in a coordinate bond both electrons are
supplied by one of the atoms.

Organic Chemistry
Empirical Formula The simplest ratio of atoms of each element in a
compound.
Molecular Formula The total number of atoms of each element in one
molecule of a compound.
Skeletal Formula A formula to show every atom and bond in a molecule.
Atoms are represented by their chemical symbol and bonds by a line between
atoms per bond.
Functional Groups Organic compounds are often made of a hydrocarbon
chain with another reactive group attached to it. This reactive group is called the
functional group. No matter the length of the hydrocarbon chain, the functional
group reacts in the same way.
Homologous Series A homologous series is a series of chemically similar
compounds which conform to a general formula. Each member of the series
differs from the next by CH2, and the members of the series show a gradation in
physical properties.
The length of the carbon chain in a homologous series does not affect the way
the molecule chemically reacts, however physical properties are affected. As the
size of a chain increases, as do the melting and boiling points due to increasing
intermolecular forces.
Isomerism Isomers are molecules with the same molecular formula but
different arrangements of the atoms.

Positional Isomers In a positional isomer, the same functional group is

in a different position in the hydrocarbon chain.
Functional Group Isomers The functional group has the same
molecular formula but a different arrangement.
Chain Isomerism The hydrocarbon chain is arranged differently.

Nomenclature
Nomenclature is the scientific naming of chemicals.

Petroleum
Petroleum or crude oil is a mixture of different organic compounds. It is a very
useful substance, used for fuel, making plastics and chemicals. Petroleum is a
viscose liquid, as the long hydrocarbon chains get tangled up. Smaller
hydrocarbon chains need to be separated from the larger chains as they are
much more useful to us as they are more volatile. This is because the smaller
the hydrocarbon chain, the less electrons and therefore less van der walls
attraction between molecules. There is less energy required to vaporise the
substance so light hydrocarbons will burn easier that heavy hydrocarbons.
Alkanes are hydrocarbon chains with the general formula C nH2n+2.
Fractional Distillation
Fractional distillation is the process by which petroleum is separated into its
fractions.
Cracking
Cracking is the process used to break less useful, long hydrocarbon chains into
smaller, more useful products. There are two types of cracking thermal and
catalytic.
Thermal cracking takes place under high temperature and pressure making it an
expensive process. The products of thermal cracking are one alkane and one or
more alkenes. It uses a free radical mechanism by breaking the covalent bond
between two carbon atoms to create free radicals free, unpaired electrons.
This is unstable, so one hydrogen atom will move to the other molecule.
Catalytic cracking uses a zeolite catalyst made from aluminium oxide and silicon
dioxide, and occurs at a lower temperature and pressure than thermal cracking.
It uses a carbocation mechanism by removing a -1 hydrogen ion to create an
unstable alkane ion, which rearranges itself in order to become more stable. The
products of catalytic cracking are branched chain alkanes and aromatic
hydrocarbons (containing a benzene ring) which are used as fuel.
Combustion
There are two types of combustion, complete and incomplete

Definitions
Relative Atomic Mass (Ar) The average mass of one atom of an element,
taking into account all naturally occurring isotopes, relative to 1/12 th of the mass
of a carbon-12 atom.
Relative Formula/Molecular Mass (Mr) The total mass of a molecule or one
formula unit of a compound, relative to 1/12th of the mass of a carbon-12 atom.
The Mole (mol) One mole of a substance is the relative mass of that
substance in grams. It helps us to avoid using very small numbers when we
measure things, which can lead to calculation error.
Calculations
Rules for Calculation

Answers should be to the same number of significant figures as the

question usually two or three.
Atomic mass is used to one decimal place.
Dont round up during calculations.

Relative Mass
To find the relative mass, the actual mass of one atom/molecule/formula unit is
divided by 1/12th of the actual mass of a carbon-12 atom.
To find the relative mass of a molecule, the masses of every atom in the
molecule are added together.
The Mole
Number of Moles (mol) = Mass (g) / Molar Mass (Mr or Ar)
Number of Moles (mol) = Concentration (mol dm-3) x Volume (dm3)
The Ideal Gas Equation
Pressure (Pa) x Volume (m3) = Number Moles (mol) x Gas Constant (8.31) x
Temperature (Kelvin, k)
PV=nRT
Kelvin is a temperature scale measured from absolute zero with an interval of
1C. 0C is equal to 273 k.
Rules for writing formulae
Metallic elements and other giant structures are written as a single atom. Most
molecular elements are diatomic, excluding Phosphorus and Sulphur, written P 5
and S8.

Ionic formulae are calculated from the charges of the ions. Ionic compounds
have no overall charge so the formulae can be calculated by balancing the
charges of the ions.

Group 1, 2 and 3 form ions with the same charge as their group number.
Group 5, 6 and 7 form ions with a charge 8 less than their group number.
Hydrogen usually forms a +1 ion, but can form a hydride ion with a charge
of -1.
Silver forms +1 ions.
Transition metals form many different charged ions, so their charge is
given in their name as a roman numeral.

Ammonium
Hydroxide
Carbonate
Hydrogen carbonate
Nitrate
Sulphate
Phosphate

NH4+
OHCO3SO42PO43-

HCO3NO3-