IB Chemistry SL and HL
IB Chemistry SL and HL
Table of contents:
Topic 3: Periodicity
Topic 13: Periodicity (HL)
Topic 4: Bonding
Topic 5: Energetics
Topic 15: Energetics (HL)
Topic 6: Kinetics
Topic 7: Equilibrium
Moles
A mole (mol) of a substance:
contains as many elementary entities (particles, atoms, molecules etc.) as there are atoms in 12
grams of pure carbon-12
is the relative atomic (or molecular or formula) mass expressed in grams
6.02 × 1023 elementary entities (Avogadro’s constant)
Molar mass
The molar mass (g mol-1) is the mass in grams of one mole of a substance.
Number of particles = number of moles × Avogadro’s constant
1.2 Formulas
1.2.1 Define the terms relative atomic mass (Ar) and relative molecular mass (Mr).
1.2.2 Calculate the mass of one mole of a species from its formula.
1.2.3 Solve problems involving the relationship between the amount of substance in moles, mass and molar mass.
1.2.4 Distinguish between the terms empirical formula and molecular formula.
1.2.5 Determine the empirical formula from the percentage composition or from other experimental data.
1.2.6 Determine the molecular formula when given both the empirical formula and experimental data.
Relative mass
Definitions
Relative atomic mass (Ar) – the relative atomic mass is the average mass of an atom,
taking into account the relative abundances of all the naturally occurring isotopes of the
element, relative to one atom of C-12. It is a relative term so it has no units.
Relative molecular mass (Mr) – the relative molecular mass is the average mass of a
molecule, calculated by adding the relative atomic masses of its constituent atoms. It is a
relative term so it has no units.
For formula units (the single units of ionic compounds), the term relative formula mass is used. The
mass of a mole of a species is the relative mass expressed in grams. The number of moles is given by:
Mass (g)
Moles (mol) =
Molar mass (g mol−1 )
Formulas
The molecular formula is the chemical formula of a substance showing the actual number of atoms of
each element in a molecule. The empirical formula is the formula in which the ratio is simplified into
the smallest integers.
Problem solving
Finding the molecular formula given the empirical formula and relative molecular
mass:
1. Use the empirical formula to find the empirical mass
2. Divide the molecular mass by the empirical mass, and round to an integer, n
3. Multiply the empirical formula by n
Theoretical yield
Theoretical yields assume that the limiting reagent is 100% used up. The actual yield is called the
experimental yield.
experimental yield
Percentage yield (%) = × 100%
theoretical yield
Limiting and excess reactants
Problem solving
If A + B → C
1. Calculate how much of reactant B (in moles) is needed to react with the amount of
reactant A provided.
2. If the amount needed is less than that provided, B is in excess and vice versa. A is
therefore the limiting reagent.
3. The difference between the amount of B needed and the amount of B provided is
equivalent to the moles of excess B.
4. The amount of product formed if A reacts completely is the theoretical yield.
Avogadro’s law
Avogadro’s law states that equal volumes of all gases under identical conditions of pressure and
temperature contain the same number of molecules i.e. the molar volume of gas A is the same as that
of gas B if the conditions (pressure and temperature) are the same. Under standard conditions (273K
and 1.013 × 105 Pa or 1 atm) the volume per mole is 22.4 dm3.
Ideal gases
The ideal gas equation is:
𝑃𝑉 = 𝑛𝑅𝑇
Where R is the gas constant which has a value of 8.31 J K-1 mol-1
The ideal gas equation implies Avogadro’s law. We can also use it to derive laws for specific cases by
moving the variables to the left hand side and the constants to the right hand side.
𝑃𝑉 𝑃1 𝑉1 𝑃2 𝑉2
Combined gas law =𝑘 =
𝑇 𝑇1 𝑇2
𝑃 𝑃1 𝑃2
Gay-Lussac’s law =𝑘 =
𝑇 𝑇1 𝑇2
Boyle’s law 𝑃𝑉 = 𝑘 𝑃1 𝑉1 = 𝑃2 𝑉2
𝑉 𝑉1 𝑉2
Charles’s law =𝑘 =
𝑇 𝑇1 𝑇2
1.5 Solutions
1.5.1 Distinguish between the terms solute, solvent, solution and concentration (g dm-3 and mol dm-3).
1.5.2 Solve problems involving concentration, amount of solute and volume of solution.
Definitions
Atomic structure
Protons and neutrons (nucleons) are found in the nucleus. Electrons are found in energy levels or
‘shells’ surrounding the nucleus.
relative relative
particle
mass charge
proton 1 +1
neutron 1 0
electron 5 × 10-4 -1
IB definitions
Mass number (A) – the mass number of an atom is the total number of protons plus
neutrons in its nucleus.
Atomic number (Z) – the atomic number of an atom is the number of protons in its nucleus.
It is also equal to the number of electrons it contains. The atomic number defines the
element and its position in the Periodic Table.
Isotopes – atoms of the same element (and so have the same atomic number, Z) but have
different numbers of neutrons (and so have different mass number, A).
Calculations
Number of protons = atomic number
Number of electrons = atomic number – charge e.g. O-2 → 8 – (-2) = 10 electrons
Number of neutrons = mass number – atomic number
Properties of isotopes
Isotopes show the same chemical properties as neutrons do not participate in chemical reactions. A
larger relative atomic mass means a larger density and a slower movement of atoms for a given
temperature. These differences affect the melting and boiling points and can be used in separation of
isotopes
Uses of radioisotopes
Uses of radioisotopes include: nuclear power generation, the sterilisation of surgical instruments in
hospitals, crime detection, finding cracks and stresses in metals and the preservation of food,
specifically:
Carbon-14 is used in carbon-dating.
Cobalt-60 is used in radiotherapy.
Iodine-131 is used as a tracer in medicine for treating and diagnosing illnesses
Uranium-235 is used for nuclear fission in power plants.
2.2 The mass spectrometer
2.2.1 Describe and explain the operation of a mass spectrometer.
2.2.2 Describe how the mass spectrometer may be used to determine relative atomic mass using the 12C scale.
2.2.3 Calculate non-integer relative atomic masses and abundance of isotopes from given data.
Calculating the Ar
Using a mass spectrum, we can find out the relative atomic mass. The relative atomic mass is equal to
the sum of the relative abundances multiplied by their respective masses divided by the sum of the
relative abundances (which should be 100 if you’re dealing with percentages):
Problems on this subject are usually quite easy; however there is one case which is not immediately
obvious: working out the abundances of isotopes given that there are only two and that you know the Ar.
The trick is that if one isotope has an abundance x, then the other must have an abundance of 100 – x,
thus there is only one variable so the problem is capable of being solved.
Problem solving
Chlorine has two isotopes – 35Cl and 37Cl and a relative atomic mass of 35.5. What are the
abundances of the two isotopes?
Let x represent the abundance of 35Cl.
𝑥 × 35 + (100 − 𝑥) × 37
35.5 =
100
35.5 × 100 = 35𝑥 + 3700 − 37𝑥
2𝑥 = 150
𝑥 = 75%
So the abundance of 35Cl is 75% and the latter is 25% abundant.
Students should be able to identify the ultraviolet, visible and infrared and variation of wavelength and
frequency across the spectrum:
A continuous spectrum shows an unbroken sequence of frequencies, such as the spectrum of visible
light. A line spectrum is an emission spectrum that has only certain frequencies of light. It is produced
by excited atoms and ions as they fall back to a lower energy level.
The Bohr model
According to the Bohr model, an electron moves into a higher energy level when it absorbs energy,
from the ground state to an excited state. This absorption produces the absorption lines. When the
electrons fall back to the ground state they emit energy, producing the emission lines. The fact that
only a few distinct colours can be observed shows there are only certain orbits in which an electron can
be placed.
∆𝐸electron = 𝐸photon = ℎ𝑓
The observed emission spectrum show above results from the energy differences between energy
levels that correspond to frequencies in the visible light region (the Balmer series). These are jumps
from higher energy levels to the second energy levels. Jumps to the first energy level (the ground state)
produce higher frequency emissions (ultraviolet) and jumps down to the third level produce lower
frequency infrared radiation. The lines converge at higher energies because the energy levels inside the
atoms become closer together.
Electron arrangement
1H 1 11Na 2, 8, 1
2He 2 12Mg 2, 8, 2
3Li 2, 1 13Al 2, 8, 3
4Be 2, 2 14Si 2, 8, 4
5B 2, 3 15P 2, 8, 5
6C 2, 4 16S 2, 8, 6
7N 2, 5 17Cl 2, 8, 7
8O 2, 6 18Ar 2, 8, 8
9F 2, 7 19K 2, 8, 8, 1
10Ne 2, 8 20Ca 2, 8, 8, 2
2000 F
N Ar
1500 Cl
C P
mol -1
Be Si
1000 H O Mg
Ca
S
500 B
Li Na Al
0 K
0 5 10 15 20
atomic number
As you can see, the first ionisation energy increases across each period, however it drops from one
period to the next due to the electron being removed from a higher energy level, but also from the
second to the third element in each period (e.g. Be to B). This is because for Be, the electron is being
removed from the s-orbital, whereas for B it is being removed from the p-orbital which has a slightly
higher energy and this more than counteracts the increase in effective nuclear charge.
Sub-level s p d f
Number of
1 3 5 7
orbitals
1 2 3 4 5 6 7 8 9 10 11 12 13
ionisation number
Energy of sub-levels
Aufbau Principle
Electrons are placed into orbitals of lowest energy first
Hund’s Third Rule
Orbitals of the same sub-level are filled singly first, then doubly – if more than one orbital in a sub-level
is available, electrons occupy different orbitals with parallel spins
1. Chromium: [Ar]3d54s1
2. Copper: [Ar]3d104s1
This occurs because the 3d and 4s sub-levels are similar in energy. Chromium’s configuration allows it
to have 6 half-filled orbitals, reducing electrostatic repulsion. This makes it a stable configuration. Half-
filled sub-levels are stable so copper also has a half filled 4s sub-level.
When positive ions are formed for transition metals, the outer 4s electrons are removed before the 3d
electrons.
Topic 3: Periodicity
3.1 The periodic table
3.1.1 Describe the arrangement of elements in the periodic table in order of increasing atomic number.
3.1.2 Distinguish between the terms group and period.
3.1.3 Apply the relationship between the electron arrangement of elements and their position in the periodic table up to Z = 20.
3.1.4 Apply the relationship between the number of electrons in the highest occupied energy level for an element and its
position in the periodic table.
The elements are arranged in the periodic table in increasing order of atomic mass from left to right.
Going down one row increase the number of electron shells by one. Going one column to the right
increases atomic mass by 1.
Group - a group is a vertical column of elements in the Periodic Table. The atoms of the elements in the
group all have the same outer shell structure but an increasing number of inner shells.
Period – a period is a horizontal row of elements in the Periodic Table. Within a period, the atoms of the
elements have the same number of shells but with an increasing number of electrons in the outer shell.
IB definitions
First ionisation energy – the first ionization energy is the minimum energy required to
remove a mole of electrons from a mole of gaseous atoms to form a mole of univalent
cations in the gaseous state. It is the enthalpy change for the reaction:
X(g) → X + (g) + e−
The atomic radius is defined as the distance from the nucleus to the outermost electron or, in practice,
half the distance between two bonded nuclei.
Trends of alkali metals
atomic radius increases down the group as there are more electron shells
ionic radius increases down the group as there are more electron shells
first ionisation energy decreases down the group as the valence electron is further from the
nucleus so the electrostatic force of attraction is weaker, and also because there is more
shielding (intermediate shells decrease the force)
electronegativity decreases because of increased distance and shielding
melting points of alkali metals decrease as atoms become larger and therefore metallic bond
becomes weaker
Trends of halogens
Halogens exhibit the same trends except that melting points increase as the van der Waals’ force
becomes greater with more electrons.
Trends across period 3
Trend Explanation
Al
nuclear charge therefore increases across
Si P S the period, pulling the energy levels closer.
Na+ Cl This means that atomic nuclei decrease
Mg2+ across the period. The same trend is
Al3+ observed with ionic radii except because the
Si4+ cations have 1 shell fewer they have a
smaller radius.
1 2 3 4 5 6 7 8
group number The graph shows the Si4+ ion (radius: 42),
the Si4- ion also exists with a radius of 271.
S
P
Mg Si
Al
Na
1 2 3 4 5 6 7 8
group number
Group 7 - halogens
they are very reactive non-metals
reactivity decreases down group
they form ionic compounds with metals and covalent compounds with other non-metals
higher halogens can displace lower ones from compounds
Formula Na2O MgO Al2O3 SiO2 P4O10 (s) SO3 (l) Cl2O7 (l)
of oxide (s) (s) (s) (s) P4O6 (s) SO2 (g) Cl2O (g)
Acid-base
basic amphoteric acidic
character
Structure giant
giant ionic molecular covalent
covalent
Period 3 oxides
P4O10 / Cl2O7 /
Oxide Na2O MgO Al2O3 SiO2 SO3 / SO2
P4O6 Cl2O
Physical liquid /
solid liquid / gas
state gas
Electrical
conductivity
high very low none
in molten
state
metal oxides are solid because they have strong ionic bonds and therefore form an ionic lattice
sulphur dioxide is a macromolecular covalent structure like diamond
the remaining three are molecular covalent
ionic compounds conduct best because of the mobile charges in molten or aqueous phase
Period 3 chlorides
Formula of AlCl3 /
NaCl MgCl2 SiCl4 PCl5 / PCl3 S2Cl2 Cl2
oxide Al2Cl6
Physical solid /
solid solid / gas liquid liquid gas
state liquid
Oxidation +1 +2 +3 +4 +5 / +3 +1 0
number
Electrical
conductivity
high poor none
in molten
state
the more polar the substance is the better it conducts; ionic compounds conduct well
the ionic compounds have the strongest forces of attraction and are therefore solid
the non-metal chlorides have dipole-dipole or van der Waals’ forces (depending on whether the
dipoles cancel)
Cl2 is non-polar so the IMFs are weak, therefore it is a gas
Reactions of period 3 chlorides with water
Chlorine reacts in a reversible disproportionation (both reduced and oxidised) reaction, producing
hydrochloric acid and chloric(I) acid:
The solution is acidic. This is why chlorine turns damp litmus paper red.
Ionic chlorides split into ions in solution, which get surrounded by water molecules (partially charged
oxygen to cation and partially charged hydrogen to anion). They become hydrated.
NaCl(s) → Na+ (aq) + Cl− (aq)
MgCl2 (s) → Mg 2+ (aq) + 2Cl− (aq)
The pH of aqueous magnesium chloride is slightly less than 7 because the Mg2+ ion is polarising.
Aluminium chloride dissociates into ions when added to water:
The aluminium ion has a high charge density due to it having a 3+ charge and a small ionic radius. The
ion attracts water molecules which form dative (or coordinate) bonds with the ion to form an
octahedral complex ion, [Al(H2O)6]3+
The hydrated ion is acidic as the Al3+ ion attracts the electrons of the OH bond of the surrounding water
molecules, and releases the H+ ion to form an acidic solution.
In summary:
Acid-base weakly
neutral acidic
character acidic
12000
ionisation energy/ kJ mol-1
10000
8000
6000
Calcium
4000 Titanium
2000
0
0 1 2 3 4 5 6
ionisation number
The increase in ionisation energies for titanium is more gradual as the 3d and 4s orbitals are close in
energy level. Titanium can exist in +2, +3 and +4 oxidation states, but not +5 because the jump in
ionisation energies is too large. Students should know that all transition elements can show an oxidation
number of +2. In addition, they should be familiar with the oxidation numbers of the following: Cr (+3,
+6), Mn (+4, +7), Fe (+3) and Cu (+1).
IB definitions
Ligand – an ion or molecule that donates a pair of electrons to a metal atom or ion in
forming a coordination complex. Ligands are Lewis bases e.g. H2O, CN-, Cl- and NH3
Complexes
Transition metal ions have relatively high charges and small sizes allowing them to attract ligands’ lone
pairs of electrons. The number of dative bonds from ligands to the central ion is called the coordination
number. Ligands can be exchanged.
Coloured complexes
In the free ion the five d orbitals are degenerate (of equal energy). However, in complexes the electric
field produced by the ligands’ lone pair of electrons causes the d orbitals to split into two levels. The
energy difference corresponds to a frequency of light. The complex absorbs, from all the frequencies
that make up white light, the frequency of light that promotes an electron from the lower to the higher
level (remember E = hf). The complexes therefore appear to be the colour complementary to the one
that is absorbed. If the d sub-level is full or empty this cannot occur e.g. Cu+, Zn2+.
Transition metals as catalysts
Transition metals act as catalysts in the following examples (specified by the syllabus):
Iron in Haber process
Vanadium(V) oxide in Contact process
Nickel in hydrogenation reactions e.g. C2H4 + H2 → C2H6
Manganese(IV) oxide (MnO2) with hydrogen peroxide (decomposition)
Palladium (Pd) and platinum (Pt) in catalytic converters
Co in vitamin B12 (needed for the production of red blood cells)
Catalysts are used in processes such as the Haber process and the Contact process to speed up
reactions and so that the same rate can be attained at a lower temperature thus saving energy and also
shifting the equilibrium to the products side (by lowering temperature).
Topic 4: Bonding
4.1 Ionic bonding
4.1.1 Describe the ionic bond as the electrostatic attraction between oppositely charged ions.
4.1.2 Describe how ions can be formed as a result of electron transfer.
4.1.3 Deduce which ions will be formed when elements in groups 1, 2 and 3 lose electrons.
4.1.4 Deduce which ions will be formed when elements in groups 5, 6 and 7 gain electrons.
4.1.5 State that transition elements can form more than one ion.
4.1.6 Predict whether a compound of two elements would be ionic from the position of the elements in the periodic table or
from their electronegativity values.
4.1.7 State the formula of common polyatomic ions formed by non-metals in periods 2 and 3.
4.1.8 Describe the lattice structure of ionic compounds.
Ionic bonding
Ionic bonding occurs between elements that have a large difference in electronegativity (typically larger
than 1.8). The atom with the low electronegativity (the metal) loses an electron and becomes a cation.
The atom with the high electronegativity (the non-metal) gains the electron and becomes an anion. As a
result there is an electrostatic attraction between the two ions.
In NaCl, for example, chlorine already has noble gas configuration (it is in the form of diatomic
molecules), but the energy given out when the ionic lattice is formed is sufficient to break the bond in
the chlorine molecule to give atoms. Each sodium atom gives an electron to a chlorine atom. In the
lattice each cation is surrounded by 6 anions and vice versa.
Common polyatomic ions
hydroxide, OH-
nitrate, NO3-
carbonate, CO32-
hydrogencarbonate, HCO3-
ethanoate, CH3COO-
sulphate, SO42-
hydrogensulphate, HSO4-
Lewis structures
In Lewis structures, lone pairs of electrons can be depicted by two crosses, two dots or a line. A bond
can be shown as a line (or double line for double bonds).
Drawing Lewis structures
1. calculate the total number of valence electrons in the molecule by multiplying the group number
of each element by the number of atoms of the element in the formula and totalling these
2. draw the skeletal structure of the molecule to show how the atoms are linked to each other
3. use pairs of crosses, dots or a single line to show one electron pair and put a pair in each bond
between atoms
4. add more electrons pairs to complete the octets around the atoms (hydrogen only needs two,
other exceptions below)
5. if there are not enough electrons, form double or triple bonds
Polar bonds
When the atoms are different the more electronegative atom exerts a greater attraction for the electron
pair, becoming more electron rich resulting in a polar bond. Bigger difference in electronegativities
means a more polar bond.
Polar molecules
For a molecule to be polar:
It must have at least one polar bond (e.g. HCl)
The polar bonds must not cancel out (e.g. methane is not polar)
VSEPR theory
VSEPR (valence shell electron pair repulsion) theory states that pairs of electrons arrange
themselves so that they are as far apart from each other as possible.
linear
2 linear 2 0
180°
trigonal
3 trigonal planar 3 0 planar
120°
v-shaped
3 trigonal planar 2 1
<120°
tetrahedral
4 tetrahedral 4 0
109.5°
pyramidal
4 tetrahedral 3 1
<109.5°
v-shaped
4 tetrahedral 2 2
<109.5°
Dipole-dipole force
Dipole-dipole occurs because polar molecules are attracted to each other by electrostatic forces. It is
stronger that Van der Waals’ but weaker than H-bonding.
Hydrogen bonding
Hydrogen bonding occurs when hydrogen is bonded directly to a small highly electronegative element,
such as fluorine, oxygen or nitrogen. As the electron pair is drawn from the hydrogen atom, it has a
small relative charge and therefore attracts a lone pair from a neighbouring molecule.
Strength of intermolecular forces
1. Hydrogen bonding
2. Dipole-dipole
3. Van der Waals’
IMFs and boiling points
The stronger the intermolecular forces, the harder it is to separate the molecules i.e. the more energy it
takes which corresponds to a higher temperature, so the stronger the IMFs, the higher the boiling point.
Metallic bonding
In the metal, the valence electrons detached from atoms creating lattice of cations. A metallic bond is
the attraction that two neighbouring cations have for delocalised electrons between them.
Properties of metals
Metals are good conductors because they contain mobile charges (free electrons)
Metals are malleable and ductile because the layers of cations can slide over each other without
breaking more bonds than are made. Impurities reduce this.
Bonding Properties
Macromolecular covalent high melting point, poor conductor (except graphite), low volatility
Some polar covalent molecules, however, in conditions where they can ionise will conduct electricity.
For example, HCl dissolved in water (hydrochloric acid) is an electrical conductor.
Solubility – like dissolves like
At the contact surface, partial charges in the water molecules are attracted to ions of opposite charge in
the lattice, which may cause them to dislodge from their position. Ions separated from the lattice in this
way become surrounded by water molecules and are said to be hydrated.
Non-polar substances (e.g. O2, N2, hydrocarbons) are not very soluble in water. Non-polar substance
can, however, dissolve in non-polar solvents owing to their ability to interact by van der Waals’ forces,
for example the halogens are readily soluble in paraffin oil.
Topic 14: Bonding (HL)
14.1 Shapes of molecules and ions
14.1.1 Predict the shape and bond angles for species with five and six negative charge centres using the VSEPR theory.
90° trigonal
5 0
120° bipryramidal
90° unsymmetrical
4 1 tetrahedron
trigonal < 120° aka see saw
5
bipryramidal
3 2 90° T-shaped
2 3 180° linear
6 0 90° octahedral
6 octahedral square
5 1 90°
pyramidal
14.2 Hybridisation
14.2.1 Describe σ and π bonds.
14.2.2 Explain hybridisation in terms of the mixing of atomic orbitals to form new orbitals for bonding.
14.2.3 Identify and explain the relationships between Lewis structures, molecular shapes and types of hybridization (sp, sp 2 and
sp3).
sp2 hybridisation
When carbon forms a double bond (e.g. C2H4), it undergoes sp2 hybridisation:
sp hybridisation
When carbon forms a triple bond (e.g. C2H2), it undergoes sp hybridisation:
Delocalisation is a characteristic of pi bonds where there is more than one possible position for a double
bond within a molecule (when there are resonance structures).
IB definitions
Exothermic reaction – An exothermic reaction is one that releases heat to the surroundings
as a result of forming products with stronger bonds than the reactants. Exothermic reactions
have a negative ΔH value.
Endothermic reaction – An endothermic reaction is one that absorbs heat from the
surroundings as a result of forming products with weaker bonds than the reactants.
Endothermic reactions have a positive ΔH value.
Standard enthalpy change of reaction – Standard enthalpy change is the heat transferred
during a reaction carried out under standard conditions:
pressure 100 kPa
temperature 298 K
all substances pure and in their standard state
Measuring enthalpy of
Measuring enthalpy of combustion
neutralisation
Enthalpy calculations
𝑄 𝑚𝑐∆𝑇
∆𝐻 = =
𝑛 𝑛
Where n is the number of moles reacted (in the combustion experiment this can be calculated from the
change in mass of the fuel burner)
Determining temperature change from graphs
You need to extrapolate backwards in order to compensate for the heat loss.
Hess’s law states that the enthalpy change for any chemical reaction is independent of the route,
provided the starting conditions and final conditions, and the reactants and products, are the same.
This means that you can work out the enthalpy of a reaction by adding and reversing several reactions.
Problem solving
IB definitions
Average bond enthalpy - The average bond enthalpy is the energy required to break a
mole of covalent bonds in the reactant, all reactants and products being in the gaseous state.
For example, X2(g) → 2X(g)
It is an average value because it takes account of the different energies in a bond between
the same atoms in different molecules.
Average bond enthalpy can also be defined as the energy released on forming a mole of
covalent bonds in the products, all reactants and products being in the gaseous state.
IB definitions
Standard state – the pure form of the substance under standard conditions of 298K (25°C)
and 1.00 × 105 Pa.
Standard enthalpy change of formation – the standard enthalpy of formation of a
substance is the enthalpy change that occurs when one mole of the substance is formed
from its elements in their standard states under standard conditions of 298K (25°C) and 1.00
× 105 Pa.
Standard enthalpy change of combustion – the standard enthalpy of combustion of a
substance is the enthalpy change that occurs when one mole of the substance burns
completely under standard conditions of 298K (25°C) and 1.00 × 105 Pa.
⊖
∆𝐻reaction = ∑ ∆𝐻𝑓⊖ (products) − ∑ ∆𝐻𝑓⊖ (reactants) ∆𝐻 = ∑ ∆𝐻𝑐⊖ (reactants) − ∑ ∆𝐻𝑐⊖ (products)
IB definitions
Lattice enthalpy – the enthalpy change that occurs when one mole of a solid ionic
compound is separated into gaseous ions under standard conditions.
Electron affinity – the enthalpy change that occurs when one mole of gaseous atoms
attracts one mole of electrons
The first electron affinity is exothermic as the electron is attracted to the positively charged nucleus. The
second, however, is endothermic as an electron is being added to an already negative atom.
Factors affecting lattice enthalpies
The energy needed to separate the ions depends on the product of the ionic
charges and the sum of the ionic radii Tip: think of the
Coulomb law
an increase in the ionic radius of one of the ions decreases the attraction equation:
between the ions 𝑞1 𝑞2
𝐹=𝑘
an increase in the ionic charge increases the ionic attraction between ions 𝑟2
Born-Haber cycles
Oxides Chlorides
𝛥𝐺 ⊖ = 𝛥𝐻 ⊖ − 𝑇𝛥𝑆 ⊖
The fact that we use standard conditions implies that the temperature is 298K.
Calculating ΔG
⊖
∆𝐺reaction = ∑ ∆𝐺𝑓⊖ (products) − ∑ ∆𝐺𝑓⊖ (reactants)
Depending on the values of ΔH and ΔS, a reaction might become spontaneous at a certain temperature.
IB definitions
Rate of reaction – the rate of increase of concentration of one of the products or the rate of
decrease of concentration of one of the reactants
Kinetics experiments
Rates of reaction can be measured by:
1. Change in volume of gas produced e.g. Mg + 2HCl → MgCl2 + H2
2. Change in mass (if a gas is produced) – same example as previous
3. Colourimetry/spectrophotometry e.g. 2HI (colourless) → H2 (colourless) + I2 (coloured)
4. Change in concentration measured using conductivity
5. Clock reactions e.g. sodium thiosulphate + hydrochloric acid
Kinetic theory
The essence of kinetic-molecular theory is that particles in a substance move randomly as a result of
the kinetic energy that they possess.
𝑇Kelvin ∝ 𝑣particle
IB definitions
Activation energy – the minimum energy required for a chemical reaction to take place
Collision theory
According to collision theory, for a reaction to occur three criteria must be met:
the particles must collide
they must collide with the appropriate geometry or orientation so that the reactive parts of the
particles come into contact
they must collide with sufficient energy (the activation energy)
Effect of increasing
Quantity Explanation
quantity
The greater the particle size, the smaller the exposed surface
area. Reactions require collisions for reactions to occur, so if
particle size decreases rate
the surface area is smaller, fewer collisions will occur per unit
time
Increasing the temperature lowers the peak of the curve and moves it to the right, more particles
have enough energy to react
Adding a catalyst reduces the activation energy, more particles have enough energy to react
Rate expression
𝐴 + 𝐵 → products
The rate constant (k) is the constant of proportionality in the rate expression. It has a specific value for
a specific reaction at a specific temperature. The units vary depending on the expressions.
The overall order of the reaction is m + n
The order with respect to a reactant is the power it is raised to in the rate expression
Initial rates method
This method involves comparing the factor by which the concentration is changed to the factor by which
the rate changes in order to determine the order with respect to the reactant
concentration multiplier order with respect to reactant = rate multiplier
So, for example, if the concentration of a reactant is doubled and the rate becomes eight times greater,
the order with respect to the reactant is 3.
Rate = k[A]3 or
Rate = k[A]2 or
Rate = k Rate = k[A] Rate = k[A][B]2 or
Rate = k[A][B]
Rate = k[A][B][C]
Most reactions that occur at a measurable rate occur as a series of simple steps. The sequence of
steps is known as the reaction mechanism. The individual steps (elementary steps) usually cannot
be observed directly. Intermediates are substances that are made in one step and used up in another.
The sum of the elementary steps should cancel to give the original equation. The term molecularity is
used in reference to an elementary step to indicate the number of reactant species involved. If a
reaction has three, four or more species combining, it is likely that it can be split into steps.
The rate-determining step
The rate equation can be known by knowing the reaction mechanism, specifically the slowest step,
which acts as a limit on the rate and is therefore called the rate-determining step.
The rate equation is also equal to the rate constant (k) multiplied by the concentrations of the
substances raised to the power of their respective coefficients in the rate-determining step.
aA + bB → products (slowstep)
Problem solving
If a species is both on the reactant and product side of the overall equation, it is probably a catalyst.
16.3 Activation energy
16.3.1 Describe qualitatively the relationship between the rate constant (k) and temperature (T).
16.3.2 Determine activation energy (Ea) values from the Arrhenius equation by a graphical method.
The rate of reaction increases with temperature (we know this already because of collision theory). A
common relationship is that 10°C increase doubles the rate. Looking back at the Maxwell-Boltzmann
distribution curve, an increase in temperature means that more particles have an energy greater or
equal to the activation energy. This means that the value of the activation energy will determine
temperature’s effect. When the Ea is larger a temperature rise will make a larger difference, and when
the Ea is smaller the temperature change will have a less significant effect.
Topic 7: Equilibrium
7.1 Dynamic equilibrium
7.1.1 Outline the characteristics of chemical and physical systems in a state of equilibrium.
5 Equilibrium can be reached from The reaction can be started with all
either direction reactants, all products or a mixture.
Equilibrium constant
Given a reversible reaction,
aA + bB ⇌ cC + dD
The equilibrium expression is the concentration of the products raised to the coefficients in the balanced
equation over those of the reactants:
[𝐶]𝑐 [𝐷]𝑑
𝐾𝐶 =
[𝐴]𝑎 [𝐵]𝑏
Le Chatelier’s principle
If any change is imposed on a system that is in equilibrium then the system tends to adjust to a new
equilibrium counteracting the change.
In an exothermic reaction heat can be considered a product, so increasing the temperature will
shift the equilibrium towards the reactants, and decreasing the temperature will shift it to the
products
In an endothermic reaction heat can be considered a reactant
Increasing pressure shifts the equilibrium to the side with fewer moles of gas, so as to decrease
the pressure
Decreasing pressure shifts it to the side with more moles of gas
Increasing concentration shifts it to the side with fewer moles of solute
Decreasing concentration shifts it to the side with more
A catalyst speeds up the reaction but does not affect the value of the equilibrium constant
Only temperature affects the value of the equilibrium constant
The Haber process
The Haber process is the process used to produce ammonia, NH3
N2 (g) + 3H2 (g) ⇌ 2NH3 (g) ∆𝐻 = −93kJ mol−1
Conditions:
catalyst iron -
Conditions:
Equilibrium of this sort requires a closed system. The liquid evaporates and the condensation rate
increases (due to more collisions on surface). When the opposite rates are equal, equilibrium is
reached.
Vapour pressure
Vapour pressure is the pressure exerted by a vapour on its liquid; however the term usually refers to
the equilibrium vapour pressure. High vapour pressure means the equilibrium lies to the right and vice
versa.
temperature
nature of substance
Temperature
For an explanation of why the vapour pressure changes with temperature, we must return to the
Maxwell-Boltzmann distribution:
Problem solving
Change -x -x x x
Equilibrium 0.03 - x 0.03 - x x x
[NO2 ][SO2 ] 𝑥2
𝐾𝐶 = = = 6.78
[SO3 ][NO] (0.03 − 𝑥)2
The thermal decomposition of water has a very small value of KC. At 1000°C, KC = 7.3 × 10-
18 for the reaction
A reaction is set up at this temperature with an initial H2O concentration of 0.10 mol dm-3.
Calculate the H2 concentration at equilibrium.
Solution
2H2O(g) = 2H2(g) + O2(g)
Equilibrium 0.10 -
2x x
2x
Effect on equilibrium
Effect on KC
expression
IB definitions
Lewis acids
Lewis acids include BF3, AlCl3, and transition metal ions in aqueous solution which accept a pair of
electrons from each of the six surrounding water molecules. This makes ligands Lewis bases.
pH below 7
react with hydroxides to form a salt
and water
react with metal oxides to form a salt pH above 7
and water alkalis are bases that dissolve in water
react with ammonia to form a salt turns litmus blue
react with metals to form a salt and
hydrogen gas
react with carbonates forming a salt,
water and carbon dioxide
turns litmus pink
barium hydroxide,
sulphuric acid, H2SO4
Ba(OH)2
Acids have a pH below 7. Neutral substances have a pH of exactly 7. Bases have a pH greater than 7.
The greater the pH the more alkaline a substance and the lower the pH the more acidic it is.
pH = − log[H + ]
This means that decreasing one pH unit represents a ten-fold increase in hydrogen ion concentration
and increasing one unit represents a ten-fold increase. A two unit change represents a one hundred-fold
change and so on.
𝐾𝑤 = 𝐾𝑐 [H2 O] = [H + ][OH − ]
pH and pOH
pH = − log[H + ]
pOH = − log[OH − ]
Weak acids
A weak acid dissociates partially in water:
Weak bases
Weak bases also dissociate partially. This can be expressed as:
Since weak acids and bases only dissociate slightly they have low Ka or Kb respectively (remember that
if the equilibrium lies to the left, Kc << 1). Since strong acids and bases dissociate fully, they will have
larger Ka or Kb respectively (remember if equilibrium lies to right, Kc >> 1).
A buffer solution is resistant to changes in pH on the addition of small amounts of strong acid or alkali.
They are a mixture of two solutions such that it contains the two species of a conjugate acid-base pair.
Acidic buffers maintain the pH below 7 and basic buffers maintain it above 7.
Factors that affect buffers
Dilution changes the buffering capacity. This depends on the molar concentrations of its
components, so decreases as they are lowered by dilution.
Temperature affects the Ka and Kb values
Calculating the pH (or pOH) of a buffer
Step 1: Write both dissociation equations:
HA ⇌ H + + A−
MA → M + + A−
Step 3: Write the equilibrium expression and rearrange depending on what you want to find:
[H + ][A− ] 𝐾𝑎 [HA]
𝐾𝑎 = → [𝐻 + ] =
[HA] [A− ]
[H + ][MA]initial 𝐾𝑎 [HA]initial
𝐾𝑎 = 𝑜𝑟 [H + ] =
[HA]initial [MA]initial
[salt] [salt]
pH = p𝐾𝑎 + log & pOH = p𝐾𝑏 + log
[acid] [base]
The pH of a salt solution depends on whether and to what extent its ions react with water and hydrolyse
it, releasing H+ or OH- ions.
Anion hydrolysis
The anion is the conjugate base of the parent acid. When the acid is weak, this conjugate is strong
enough to hydrolyse water:
A− (aq) + H2 O(l) ⇌ HA(aq) + OH − (aq)
The leftmost and rightmost points represent the pH of the acid and base respectively
the big vertical jump is the point of inflection
the equivalence point is where the solutions neutralise
pH = pKa or pOH = pKb at the half-equivalence point
when a weak acid is added to a weak base, it is difficult to determine the equivalence point.
Instead other techniques are used.
18.5 Indicators
18.5.1 Describe qualitatively the action of an acid–base indicator.
18.5.2 State and explain how the pH range of an acid–base indicator relates to its pKa value.
18.5.3 Identify an appropriate indicator for a titration, given the equivalence point of the titration and the pH range of the
indicator.
Indicators are weak acids or weak bases in which the undissociated and dissociated forms have
different colours.
HIn(aq) ⇌ H + (aq) + In− (aq)
colour A colour B
Le Chatelier’s principle
Increasing the H+ concentration moves the equilibrium to the left
Increasing the OH- concentration moves the equilibrium to the right
Colour change
Indicators change colour when the pH is equal to their pKa, at the midpoint in the equilibrium, so that
[HIn] = [In-]
[H+ ][In− ] [H + ][In− ]
𝐾𝑎 = = → p𝐾𝑎 = pH
[HIn] [HIn]
This is known as the change point or the end point of the indicator. At this point, the addition of a very
small volume of acid or base will shift the equilibrium as described above, and so cause the indicator to
change colour.
Choosing the appropriate indicator
An indicator will be effective in signalling the equivalence point of a titration when its end point coincides
with the pH at the equivalence point.
no significant change in pH at
weak acid + weak base
equivalence
IB definitions
Oxidation – the loss of an electron, the gain of oxygen, the loss of hydrogen or the increase
in oxidation number
Reduction – the gain of an electron, the loss of oxygen, the gain of hydrogen or the
decrease in oxidation number
Writing half-equations
1. Balance the atoms other than H and O
2. Balance each half-equation for O by adding H2O as needed.
3. Balance each half-equation for H by adding H+ as needed.
4. Balance each half-equation for charge by adding electrons to the sides with the more positive
charge.
Writing the redox equation
5. Equalize the number of electrons in the two-half equations by multiplying each appropriately.
Add the two half-equations together, cancelling out anything that is the same on both sides, which
includes electrons.
IB definitions
Oxidising agent – a substance that readily oxidizes other substances. Oxidizing agents are
thus reduced
Reducing agent – a substance that readily reduces other substances. Reducing agents are
thus oxidized.
9.3 Reactivity
9.3.1 Deduce a reactivity series based on the chemical behaviour of a group of oxidizing and reducing agents.
9.3.2 Deduce the feasibility of a redox reaction from a given reactivity series.
More reactive metals are stronger reducing agents than less reactive metals. A more reactive metal is
able to reduce the ions of a less reactive metal. More reactive non-metals are stronger oxidising agents
than less reactive non-metals. A more reactive non-metal is able to oxidise the ions of a less reactive
non-metal.
If zinc is placed in a copper (II) sulphate solution, electrons are transferred spontaneously from the zinc
to copper and energy is released as heat. Instead of being lost as heat, the energy can be available as
electrical energy by separating the two half-reactions into half-cells and allowing the electrons to flow
through a circuit. This is known as an electrochemical, galvanic or voltaic cell.
Half cells generate electrode potentials: when a metal is placed in a solution containing its ions, an
equilibrium forms between the oxidised and normal forms. As atoms become ions they leave their
electrons behind them creating a charge separation or electrode potential, the size of which is
determined by the position of the equilibrium. In general, the more reactive a metal, the more negative
its electrode potential in its half-cell. Half-cells connected by a wire are called electrodes. Oxidation
always occurs at the anode; reduction always occurs at the cathode. In the voltaic cell, the anode has
a negative charge and the cathode has a positive charge. Electrons flow from the anode to cathode. A
salt bridge is a glass tube that contains an aqueous solution of ions that enables negative charge to be
carried in the opposite direction to that of the electrons (from cathode to anode). This ion movement
neutralises any build up of charge and maintains the pd.
Notation
The notation used for describing electrochemical cells is:
An electrolytic cell uses an external source of voltage to bring about a redox reaction that would
otherwise be non-spontaneous. The reactant is known as the electrolyte – a molten liquid or aqueous
solution of an ionic compound. As the electric current passes through it, redox reactions occur at the
electrodes, removing the charges of the ions or ‘discharging’ them. Oxidation occurs at the positive
electrode (anode) – anions lose electrons - and reduction occurs at the negative electrode (cathode) –
positive ions gain electrons.
The current is not passed through the electrolyte by electrons but by the ions as they are mobile.
the electrode is coated in very fine platinum (also known as platinum black)
the large surface area makes the reaction happen readily
platinum is also fairly inert and can also catalyse the proton reduction
Standard electrode potential
When the standard hydrogen electrode is connected to another standard half-cell by an external circuit
with a high resistance voltmeter and a salt bridge, the emf generated is known as the standard
electrode potential of the half-cell.
The values inserted into this equation must be reduction potentials. The stoichiometry of the equation
does not matter.
If 𝐸 ⊖ cell is positive, the reaction is spontaneous as written; if 𝐸 ⊖ cell is negative, the reaction is non-
spontaneous and in fact the reverse reaction is spontaneous.
19.2 Electrolysis
19.2.1 Predict and explain the products of electrolysis of aqueous solutions.
19.2.2 Determine the relative amounts of the products formed during electrolysis.
19.2.3 Describe the use of electrolysis in electroplating.
In this electrolysis of water, twice the number of moles (and because of Avogadro’s law, twice the
volume too) of hydrogen will be produced than of oxygen.
Determining the actual amounts of product*
This isn’t actually on the syllabus. The yield depends on three quantities
charge of the ion
the current
duration (time)
Charge is the product of current and time:
𝑄 =𝐼∙𝑡
Problem solving
If a current of 2.00 amps is passed through a solution of CuSO4 for 10 minutes, how many
moles of Cu are formed?
60s 1mol(e− ) 1mol(Cu)
10min × × 2.00A × × = 0.00622 (3 significant figures)
1min 96500C 2mol(e− )
Electroplating
Electroplating is the process of using electrolysis to deposit a layer of
a metal on top of another metal or other conductive substance. An
electrolytic cell used for electroplating has the following features:
an electrolyte containing the metal ions to be deposited
the object to be plated as the cathode
sometimes the anode is made of the same metal which is to be
coated because it may be oxidised to replenish the supply the
ions in the electrolyte
Electroplating can be used for various purposes:
decorative purposes
corrosion control e.g. zinc is deposited on iron or steel in a process called galvanisation. This is
called sacrificial protection.
improvement of function e.g. electroplating of chromium on steel improves the wear on steel
parts such as hand tools or crankshafts
Homologous series
The main features of a homologous series are:
1. Successive members of a homologous series differ by one CH2 group
2. All members of a homologous series can be expressed by the same general formula
3. Successive members show a gradation in physical properties
4. The different members have similar chemical properties
The boiling points increase as the chain gets longer as the van der Waals forces get stronger.
Formulas
The empirical formula shows the simplest ratio of atoms in a compound.
The molecular formula shows the actual number of atoms in a compound.
The structural formula is a representation of a molecule showing how the atoms are bonded together.
Structural isomers
Structural isomers are compounds with the same molecular formula but with different arrangements of
atoms, for example the isomers of hexane are:
hexane 2-methylpentane 3-methylpentane
2,2-dimethylbutane 2,3-dimethylbutane
Homologous Functional
Prefix Suffix
series group
fluoro-, chloro,
Halogen alkane C−X
bromo-, iodo-
acid halide
Volatility
We can summarise the effect on volatility of the different functional groups as follows.
most volatile least volatile
alkane > halogenoalkane > aldehyde > ketone >
alcohol > carboxylic acid
van der Waals’ → dipole-dipole → hydrogen bonding
increasing strength of molecular attraction →
increasing boiling point →
Solubility
Molecules with functional groups that enable hydrogen bonds to form with water include the alcohols,
the carboxylic acids and the amines. So the smaller members of these series are readily soluble in
water. Aldehydes, ketones, amides and esters are less soluble, while halogenoalkanes, alkanes and
alkenes are insoluble.
10.2 Alkanes
10.2.1 Explain the low reactivity of alkanes in terms of bond enthalpies and bond polarity.
10.2.2 Describe, using equations, the complete and incomplete combustion of alkanes.
10.2.3 Describe, using equations, the reactions of methane and ethane with chlorine and bromine.
10.2.4 Explain the reactions of methane and ethane with chlorine and bromine in terms of a free-radical mechanism.
When the oxygen supply is limited, alkanes undergo incomplete combustion, to produce carbon
monoxide and water or carbon and water if the supply is even more limited:
2C3 H8 (g) + 7O2 (g) → 6CO(g) + 8H2 O(g)
C3 H8 (g) + 2O2 (g) → 3C(s) + 4H2 O(g)
The UV light is needed to break the covalent bond in the chlorine molecule. This creates two free
radicals i.e. two chlorine atoms each with an unpaired electron. This is the start of a reaction described
by a reaction mechanism.
1. Initiation
The homolytic fission of the chlorine molecule:
UV light
Cl2 → 2Cl ∙
2. Propagation
For example:
Cl ∙ +CH4 → CH3 ⋅ +HCl
CH3 ∙ +Cl2 → CH3 Cl + Cl ∙
CH3 Cl + Cl ∙ → CH2 Cl ∙ +HCl
CH2 Cl ∙ +Cl2 → CH2 Cl2 + Cl ∙
These reactions are called propagation because they both use and produce free radicals.
3. Termination
Cl ∙ +Cl ∙ → Cl2
CH3 ∙ +Cl ∙ → CH3 Cl
CH3 ∙ +CH3 ∙ → C2 H6
10.3 Alkenes
10.3.1 Describe, using equations, the reactions of alkenes with hydrogen and halogens.
10.3.2 Describe, using equations, the reactions of symmetrical alkenes with hydrogen halides and water.
10.3.3 Distinguish between alkanes and alkenes using bromine water.
10.3.4 Outline the polymerization of alkenes.
10.3.5 Outline the economic importance of the reactions of alkenes.
With hydrogen
Hydrogenation occurs in the presence of a nickel catalyst at 150°C e.g.
H H H H H H
Ni catalyst
∣ ∣ ∣ 150°C
∣ ∣ ∣
H − C − C = C − H + H2 → H− C−C −C −H
∣ ∣ ∣ ∣ ∣ ∣
H H H H H H
propene + hydrogen → propane
With halogens
Dihalogeno compounds are produced in the reactions between halogens and alkenes. These reactions
happen quickly at room temperature accompanied by the loss of colour of the halogen e.g.
H H H H H H
∣ ∣ ∣ fffffffff ∣ ∣ ∣
H − C − C = C − H + Br2 → H− C − C − C −H
∣ ∣ ∣ ∣ ∣ ∣
H H H H Br Br
propene + bromine → 1,2-dibromopropane
With hydrogen halides
The hydrogen halide (HX) with the weaker bond reacts faster. This means the reaction rate increases
down the group. This takes place rapidly at room temperature e.g.
H H H H H H
∣ ∣ ∣ fffffffff ∣ ∣ ∣
H − C = C − C − H + HCl → H−C − C − C−H
∣ ∣ ∣ ∣ ∣ ∣
H H H H Cl H
The halide bonds to the carbon with fewer hydrogens bonded to it.
With water
Hydration is the reaction that converts an alkene into an alcohol. Conditions: heat with steam and
catalyst of concentrated sulphuric acid.
Polymerisation
Alkenes (the monomers) can join together to produce long chains called polymers by addition.
The hydration of ethene is of industrial significance because ethanol is a very important solvent and so
is manufactured on a large scale. The hydrogenation reaction is used in the margarine industry to
saturate oil compounds, making the liquid solid. Polymers have many uses, for example:
Polymer Example of uses
polythene plastic bags
polychloroethene
water pipes
(PVC)
polypropene ropes
polystyrene packaging and insulation
Teflon
non-stick frying pans
(polytetrafluoroethene)
nylon tents
clothing (especially mixed
terylene
with cotton)
10.4 Alcohols
10.4.1 Describe, using equations, the complete combustion of alcohols.
10.4.2 Describe, using equations, the oxidation reactions of alcohols.
10.4.3 Determine the products formed by the oxidation of primary and secondary alcohols.
Combustion
When alcohols undergo complete combustion (when oxygen is plentiful), the products are water and
carbon dioxide:
2CH3 OH(l) + 3O2 (g) → 2CO2 (g) + 4H2 O(g)
Oxidation
Combustion involves the complete oxidation of the alcohol molecules, but it is also possible for them to
react with oxidising agents which selectively oxidise the carbon atom attached to the OH group, keeping
the carbon skeleton intact, so that useful compounds can be made. In the lab, acidified potassium
dichromate(VI) is used as the oxidising agent. Owing to the Cr(VI), this solution is bright orange. When
the mixture is heated, the colour changes to green as the Cr(VI) is reduced to Cr(III). The oxidising
agent is usually represented by +[O].
Primary alcohols
Primary alcohols are oxidised in a two-step reaction, first forming the aldehyde and then the carboxylic
acid:
H H H O H O
∣ ∣ +[O], heat ∣ ∥ +[O], heat ∣ ∥
H − C − C − OH → H− C −C −H → H − C − C − OH
∣ ∣ ∣ ∥ reflux ∣ ∥
H H H O H O
Secondary alcohols
Secondary alcohols are oxidised to the ketone:
H H H H H H
∣ ∣ ∣ +[O], heat ∣ ∣ ∣
H− C− C −C −H → H− C − C − C −H
∣ ∣ ∣ reflux ∣ ∥ ∣
H OH H H O H
propan-2-ol → propanone
Tertiary alcohols
Tertiary alcohols are not readily oxidised under similar conditions, as this would involve breaking the
carbon skeleton of the molecule, which requires significantly more energy: no colour change.
10.5 Halogenalkanes
10.5.1 Describe, using equations, the substitution reactions of halogenoalkanes with sodium hydroxide.
10.5.2 Explain the substitution reactions of halogenoalkanes with sodium hydroxide in terms of S N1 and SN2 mechanisms.
Substitution
In a halogenoalkane, the C-X bond is polar because the halogen is more electronegative. As a result
the halogen gains a partial negative charge (δ-), whereas the carbon gains a partial positive charge (δ+)
and is said to be electron deficient. Nucleophiles are reactants that are themselves electron rich (they
have a lone pair of electrons or they are anions) such as H2O, OH-, NH3 and CN-. SN stands for
nucleophilic substitution.
Primary halogenoalkanes: SN2 mechanism
Primary halogenoalkanes have at least two hydrogen atoms attached to the carbon with the C-X bond
e.g.
H
∣
H − C − Cl
∣
H
The overall reaction with NaOH is:
CH3 Cl + OH − → CH3 OH + Cl−
As the hydrogen atoms are so small, the carbon atom is relatively open to attack by the nucleophile. An
unstable transition state is formed in which the carbon is weakly bonded simultaneously to both the
halogen and the nucleophile. The C-X bond breaks heterolytically, releasing X- and forming the product.
This is known as a bimolecular reaction because the rate is dependent on both the concentration of the
halogenoalkane and of the hydroxide ion. It is called SN2: substitution nucleophilic bimolecular.
The presence of the alkyl groups around the carbon of the C-X bond causes steric hindrance, meaning
that these bulky groups make it difficult for an incoming group to attack this carbon atom. The first
reaction involves the C-X bond breaking heterolytically. The carbon is left with a positive charge. It is
called a carbocation. This is then attacked by the nucleophile in the second step.
A factor which favours this mechanism in tertiary halogenoalkanes is that the carbocation is stabilised
by the presence of the three alkyl groups, as each of these has an electron-donating or positive
inductive effect, shown by the blue arrows in the diagram above. This stabilising effect helps the
carbocation to persist for long enough for the second step to occur.
This is a unimolecular reaction.
Secondary halogenoalkanes
Secondary halogenoalkanes undergo both SN1 and SN2 mechanisms.
H H H H
∣ ∣ ∣ ∣
H − C − C − Br + NH3 → H − C − C − NH2 + HBr
∣ ∣ ∣ ∣
H H H H
This reaction is usually carried out using concentrated ammonia solution in a sealed tube that raises
the pressure. Because amines, like ammonia, have a lone pair of electrons, they can also behave as
nucleophiles and so react to form further substituted products. Increasing the concentration of the
ammonia will, however, decrease the amounts of these other products.
Conversion into nitrile
The cyanide ion contains a lone pair of electrons and a negative charge on the carbon atom:
[× × −
×C ≡ N× ]
The reactions take place when the halogenoalkane is heated under reflux with a solution of
potassium cyanide in ethanol. The alcohol acts as a solvent for both the polar and non-polar
components of the reaction mixture.
When the substitution reaction occurs, the compound gains a carbon atom. This is therefore one of the
most convenient methods for increasing the chain length. Reduction of this group using hydrogen and a
metal catalyst such as nickel converts it into a primary amine.
Ni
C2 H5 CN + 2H2 → C2 H5 CH2 NH2
Elimination
An elimination reaction involves the removal of a small molecule from a larger molecule. It results in the
formation of a C=C bond.
X Y
∣ ∣ ∣ ∣
−C−C− → −C = C− + X−Y
∣ ∣ ∣ ∣
X Y
The reaction is usually carried out in the presence of a hot alcoholic solution of a base such as sodium
hydroxide.
alcoholic solvent
CH3 CH2 CH2 Br + NaOH → CH3 CH = CH2 + NaBr + H2 O
E2 mechanism
This proceeds by the OH- ion acting as a base and accepting a proton, H+, from the bromopropane. The
carbon-bromine bond splits heterolytically with both the electrons going to the bromide ion. The
electrons from the carbon-hydrogen bond form the new bond of the double bond.
E1 mechanism
An alternate mechanism would involve the ionisation of the halogenoalkane by loss of the halide ion
occurring as the first slow step in a two-step process. This is followed by loss of the proton and
formation of the double bond in a second, faster step.
H H H H H H
∣ ∣ ∣ slow ∣ ∣ ∣
H− C − C − C −H → H − C − C − C − H + Br −
⤹∣⤸ ⤹∣⤸ ⤹∣⤸ ∣ ∣ +
H H Br H H ∣
H H H H H H
∣ ∣ ∣ fast ∣ ∣ ∣
H− C − C − C −H → H − C − C = C − H + H+
∣ ∣ + ∣ ∣ ∣
H H ∣ H H H
A condensation reaction occurs when two molecules react to form a product with the loss of a small
molecule.
Esters
Carboxylic acids and alcohols condense to form esters (this is called esterification)
The name of the ester takes the name of the alkyl portion of the alcohol followed by the name of the
acid salt (e.g. methanol + ethanoic acid gives methyl ethanoate, if you can’t remember that, then recall
that sodium hydroxide + ethanoic acid gives sodium ethanoate). This reaction is usually carried out by
warming a mixture of the carboxylic acid and alcohol in the presence of concentrated sulphuric acid.
Esters have no hydrogen bonding and so are more volatile and less soluble in water than the parent
acid and alcohol. Many esters have sweet, fruity smells and are used in food flavourings and perfumes.
Some are used as plasticisers, helping to soften plastics and make them more flexible.
O
H2 SO4 (conc)
∥
X − COOH + HO − Y → X − C − O − Y + H2 O
∥
O
Polyesters
The product of a diacid (two OH groups) and a dicarboxylic acid (two COOH groups) is a polyester.
O O
∥ ∥
𝑛 × HOOC − X − COOH + 𝑛 × HO − Y − OH → −X − C − O − Y − O − C − + 𝑛H2 O
∥ ∥
( O O )𝑛
Amides
Carboxylic acids and amines condense to form amides.
O O
∥ ∥
X − COOH + H2 N − Y → X − C − N − Y + H2 O
∥ ∣
O H
Polyamides
The product of diamines and diacids is a polyamide.
O O O O
∥ ∥ ∥ ∥
𝑛 × HOOC − X − COOH + 𝑛 × H2 N − Y − NH2 → −X − C − N − Y − N − C + 𝑛H2 O
∥ ∣ ∣ ∥
( O H H O) 𝑛
Many synthetic polyamides have been produced such as Kevlar. They are widely used in the textiles
industry for clothing and carpets, as well as machine parts, tyre cords, and ropes.
Stereoisomerism
Stereoisomers differ from each other in the spatial arrangement of their atoms. There are two types of
stereoisomerism in the IB: geometric (cis-trans) and optical isomerism.
Physical properties
The physical properties depend on various factors, including:
the polarity of the molecules
the shape or symmetry of the molecules
cis-1,2- trans-1,2-
dichloroethene dichloroethene
net dipole non-polar molecule
boiling point 60°C boiling point 48°C
melting point -80°C melting point -50°C
The boiling point of the cis isomer is higher because the molecule has dipole-dipole forces of attraction
as well as van der Waals’. The melting point is generally more influenced by the symmetry of the
molecules as this affects the packing in the solid state, therefore the trans isomers has the higher
melting point.
Chemical properties
The chemical properties of geometric isomers are usually very similar. An exception is butenedioic acid.
When the trans isomer is heated it sublimes, but does not react chemically.
Optical isomers
A carbon atom bonded to four different atoms or groups is known as asymmetric or chiral. Optical
isomers are non-superimposable mirror images of a molecule. A mixture containing equal amounts of
the two enantiomers is known a racemic mixture.
Optical isomers have identical chemical and physical properties with two exceptions:
optical activity
reactivity with other chiral molecules
Optical activity
Ordinary light consists of electromagnetic waves that oscillate in an infinite number if planes at right
angles to the direction of travel. When passed through a polariser, only the light waves oscillating in a
single plane pass through. This is plane-polarised light. The amount and direction of rotation can be
measured with a polarimeter. The light that comes out of the solution passes through a second polariser
called an analyser, which is rotated until the maximum amount of light passes through. In order to
compare different solutions, the concentrations, the wavelength of light used and the sample path-
length must all be kept the same.
Optical isomers rotate plane-polarised light in equal amounts but in opposite directions. A racemic
mixture is optically inactive.
Given a measurement 5 ± 1,
the absolute uncertainty is ± 1
the percentage uncertainty is 20%
Calculating uncertainties
When adding or subtracting, the uncertainties are added together.
𝐴+𝐵 = 𝐶 → ∆𝐶 = ∆𝐴 + ∆𝐵
When multiplying or dividing, percentage uncertainties are added and the result is multiplied by the
value to get the absolute uncertainty.
∆A ∆𝐵
𝐴 ×𝐵=𝐶 → ∆𝐶 = 𝐶 × ( + )
𝐴 𝐵
-
Option B: Human biochemistry
B1 Energy
B.1.1 Calculate the energy value of a food from enthalpy of combustion data.
Bomb calorimeter
B2 Proteins
B.2.1 Draw the general formula of 2-amino acids.
B.2.2 Describe the characteristic properties of 2-amino acids
B.2.3 Describe the condensation reaction of 2-amino acids to form polypeptides.
B.2.4 Describe and explain the primary, secondary (α-helix and β-pleated sheets), tertiary and quaternary structure of proteins.
B.2.5 Explain how proteins can be analysed by chromatography and electrophoresis.
B.2.6 List the major functions of proteins in the body.
They are called 2-amino acids because the chain is numbered starting with the carboxylic acid group.
The amino group is therefore attached to carbon 2.
Properties of 2-amino acids
Amino acids are crystalline compounds with high melting points, usually above 200 °C, and have much
greater solubility in water than in non-polar solvents. These properties are typical of ionic compounds
and suggest that amino acids exist as dipolar ions (having both positive and negative charges on the
same group of atoms) known as zwitterions. The fact that amino acids usually move in an electric field
is further evidence of the existence of charges within their structure.
Since they contain both acid and base groups, amino acids are amphoteric.
As an acid, donating H+,
At the isoelectric point, with no net charge at this pH, amino acids will not move in an electric field. Also
at this point, the molecules will have minimum mutual repulsion and so be the least soluble.
Analysis of proteins
The first step in protein analysis is hydrolysing the protein into its component amino acids. This is not
the same as the primary structure as you will not know the sequence of the amino acids.
Chromatography
The procedure is simple to run. A small sample of the amino acid mixture is spotted near the bottom of
some chromatographic paper and this position, known as the origin, clearly marked (in pencil so as not
to interfere with the experiment). The paper is then suspended in a chromatographic tank containing a
small volume of solvent, ensuring that the spot is above the level of the solvent.
As the solvent rises up the paper by capillary action it will pass over the spot. Amino acids in the spot
will distribute themselves between two phases – the stationary phase (the water in the paper) and the
mobile phase (the solvent) to different extents and so move up the paper at different speeds. They will
therefore become spread out according to their different solubilities.
When the solvent reaches almost to the top of the paper, its final position is marked and is known as the
solvent front. The paper is removed from the tank and developed by spraying it with the locating
reagent ninhydrin.
From the results you can calculate the Rf value (retention factor).
distance moved by amino acid
Rf =
distance moved by solvent
Electrophoresis
Electrophoresis is a technique for the analysis and separation of a mixture based on the movement of
charged particles in an electric field. As we learned earlier, amino acids carry different charges
depending on the pH and so can be separated by this means when placed in a buffered solution.
In gel electrophoresis, the medium is a gel, typically made of polyacrylamide. The amino acid mixture is
placed in wells in the centre of the gel and an electric field is applied. Depending on the pH of the buffer
used, different amino acids will move at different rates towards the oppositely charged electrodes. At
their isoelectric point, amino acids will not move as they carry no net charge. When separation is
complete they can be detected by a stain or made to fluoresce under UV light and identified from their
position using data tables.
Electrophoresis can also be used to separate and identify intact proteins according to their different
rates of migration towards the poles.
B3 Carbohydrates
B.3.1 Describe the structural features of monosaccharides.
B.3.2 Draw the straight-chain and ring structural formulas of glucose and fructose.
B.3.3 Describe the condensation of monosaccharides to form disaccharides and polysaccharides.
B.3.4 List the major functions of carbohydrates in the human body.
B.3.5 Compare the structural properties of starch and cellulose, and explain why humans can digest starch but not cellulose.
B.3.6 State what is meant by the term dietary fibre.
B.3.7 Describe the importance of a diet high in dietary fibre.
Structure of monosaccharides
All carbohydrates have the general formula Cx(H2O)y. Monosaccharides have the empirical formula
CH2O (x = y). They contain a carbonyl group (C=O) and at least two OH groups. The large number of
polar groups makes them readily soluble in water.
Straight-chain Ring
The ring structure restricts rotation and allows for geometric (cis-trans) isomers known as α-glucose and
β-glucose.
Starch
Starch is a polymer of α-glucose, used as the main storage carbohydrate in plants. Starch is a mixture of
amylase (1-4 linked α-glucose molecules) and amylopectin (1-4 and 1-6 linked α-glucose molecules).
Starch is a spiral structure.
Glycogen
Glycogen is like amylopectin but with many more 1-6 glycosidic branches.
Cellulose
Cellulose is a polymer of β-glucose molecules. It has 1-4 links called β-glycosidic links. These position
the sugars at a different angle from the α-glycosidic links found in amylase and amylopectin so the
cellulose chain forms an uncoiled linear structure with alternate glucose monomers ‘upside down’ with
respect to each other.
Starch Cellulose
made from α-glucose made from β-glucose
spiral structure uncoiled linear structure
Functions of carbohydrates
glucose and fructose are the main substrates for respiration
they are also used in the synthesis of larger molecules (e.g. fats, nucleic acids, amino acids)
glycogen is used for energy storage in the liver and muscles
cellulose makes up dietary fibre
Dietary fibre
The human body produces the enzymes to hydrolyse starch and cellulose. The enzyme needed to
break down the β-glycosidic links (cellulose) found in cellulose are not produced by the body. Cellulose
makes up dietary fibre. Dietary fibre is needed for the health of the large intestine. The cellulose fibrils
abrade the wall of the digestive tract and stimulate the lining to produce mucus. This helps in the
smooth passage of undigested food through the gut and so helps to reduce conditions such as
constipation and the related conditions hemorrhoids (bleeding of the wall of the rectum) and irritable
bowel syndrome. There is also evidence that it may be helpful in preventing the development of
colorectal cancer.
B4 Lipids
B.4.1 Compare the composition of the three types of lipids found in the human body.
B.4.2 Outline the difference between HDL and LDL cholesterol and outline its importance.
B.4.3 Describe the difference in structure between saturated and unsaturated fatty acids.
B.4.4 Compare the structures of the two essential fatty acids linoleic (omega–6 fatty acid) and linolenic (omega–3 fatty acid) and
state their importance.
B.4.5 Define the term iodine number and calculate the number of C=C double bonds in an unsaturated fat/oil using addition
reactions.
B.4.6 Describe the condensation of glycerol and three fatty acid molecules to make a triglyceride.
B.4.7 Describe the enzyme-catalysed hydrolysis of triglycerides during digestion.
B.4.8 Explain the higher energy value of fats as compared to carbohydrates.
B.4.9 Describe the important roles of lipids in the body and the negative effects that they can have on health.
Triglycerides
Triglycerides are the major constituent of fats and oils. They are esters formed by
condensation reactions between glycerol (propane-1,2,3-triol) and three fatty acids.
Each glycerol condenses with three fatty acids and eliminates three water molecules.
Phospholipids
Phospholipids are like triglycerides but the third -OH position of the glycerol has,
instead, condensed with a phosphate group. Different phospholipids vary in their fatty
acid chains and in the group attached to the phosphate.
Phospholipids are characterized by having a polar, or hydrophilic ‘head’ (the phosphate group) and two
non-polar, or hydrophobic ‘tails’ (the hydrocarbon chains of the fatty acids). As a result they will
spontaneously form a phospholipid bilayer which maximizes the interactions between the polar
groups and water, while creating a non-polar, hydrophobic, interior.
Steroids
Steroids are lipids with a structure consisting of four fused rings e.g. cholesterol:
The 120° bond angles caused by the C=C bonds create kinks in the chain, making them pack less
densely. Unsaturated triglycerides have weaker IMFs and are liquids at room temperature, known as
oils. There is a strong correlation between diets rich in saturated fats and elevated levels of LDL.
IB definitions
The iodine number of a fat is defined as the number of grams of iodine which reacts with 100
g of fat.
Unsaturated fatty acids undergo addition reactions with iodine, adding an iodine atom to each of the two
carbons in the C=C bond.
I I
∣ ∣ ∣ ∣
− C = C − + I2 → − C − C −
∣ ∣ ∣ ∣
X Y
Problem solving
Digestion of fats
Fats and oils are insoluble therefore must be broken down into their component molecules in the gut
during digestion. This involves hydrolysis reactions involving water and lipases.
Vitamins
Vitamins with many polar bonds are water soluble e.g. vitamin C. Those which are more non-polar are
fat soluble e.g. vitamin A and D.
Nutrient deficiencies
General solutions:
• providing food rations that are composed of fresh and vitamin- and mineral-rich foods
• adding nutrients missing in commonly consumed foods
• genetic modification of food
• providing nutritional supplements
• providing selenium supplements to people eating foods grown in selenium-poor soil.
B6 Hormones
B.6.1 Outline the production and function of hormones in the body.
B.6.2 Compare the structures of cholesterol and the sex hormones.
B.6.3 Describe the mode of action of oral contraceptives.
B.6.4 Outline the use and abuse of steroids.
Hormones are chemical messengers. They are secreted directly into the blood by endocrine glands.
Endocrine gland Hormone Functions
increase uptake of water, so raises the concentration of
anti-diuretic hormone
pituitary gland urine; important in the control of osmotic potential of the
(ADH)
blood
regulation of the basal metabolic rate, growth and
thyroid gland thyroxine
development
increases uptake of Na+ by the kidneys and so
adrenal cortex aldosterone important in the control of Na+ and K+ ratios in fluids;
raises blood pressure
raises blood glucose level, increases rate and force of
adrenal medulla adrenaline heartbeat and increases blood supply to heart and
skeletal muscles
decreases blood glucose level by increasing uptake
pancreas insulin and utilisation by cells; increases glucose to glycogen
conversion in the liver
oestrogen and development of secondary female characteristics,
ovary
progesterone menstrual cycle
testes testosterone development of secondary male characteristics
B7 Hormones
B.7.1 Describe the characteristics of biological catalysts (enzymes).
B.7.2 Compare inorganic catalysts and biological catalysts (enzymes).
B.7.3 Describe the relationship between substrate concentration and enzyme activity.
B.7.4 Determine Vmax and the value of the Michaelis constant (Km) by graphical means and explain its significance.
B.7.5 Describe the mechanism of enzyme action, including enzyme substrate complex, active site and induced fit model.
B.7.6 Compare competitive inhibition and non-competitive inhibition.
B.7.7 State and explain the effects of heavy metal ions, temperature changes and pH changes on enzyme activity.
Characteristics of enzymes
Enzymes are proteins, typically containing several hundred amino acids. They have a well-defined
tertiary structure and so are globular proteins, soluble in water.
The maximum rate (Vmax) varies from one enzyme to another and depends on the temperature and pH
conditions. It has the units of rate.
The Michaelis constant (Km) is the substrate concentration at which the rate is ½ its maximum value. It
has the units of concentration. It varies with pH and temperature. The value of Km gives information
about the affinity of the enzyme for its substrate. It is an inverse relationship - a low value of Km means
that the reaction is going quickly even at low substrate concentrations. A higher value means that the
enzyme has a lower affinity for its substrate
Enzyme-substrate complex
Enzymes are biological catalysts that increase the rate of reaction without themselves being affected, by
offering an alternative reaction pathway. The substrate binds to the enzyme at the active site to form an
enzyme substrate complex. This depends on the compatibility of the R groups at the active site. The
interactions involve hydrophobic interactions, dipole-dipole attractions, hydrogen bonds and ionic
attractions. The binding in the complex puts a strain on the substrate molecule, and so facilitates the
breaking and the forming of bonds.
Induced-fit mechanism
This suggests that in the presence of the substrate, the active site undergoes some conformational
changes, shaping itself to allow a better fi t. So instead of the substrate fitting into a rigid active site, this
is a more dynamic relationship in which the amino acid R groups at the active site change into the
precise positions that allow the binding to occur.
Temperature
Increasing the temperature increases the frequency of collisions and therefore increases the rate. After
a certain point, the effect of the increase in kinetic energy is to change the conformation of the protein
by disrupting the bonds and forces responsible for holding it in its tertiary structure. This is
denaturation. Lowering the temperature causes deactivation, but this is usually reversible.
pH
Changes in pH represent changes in the hydrogen ion concentration, and this affects the equilibrium
positions of ionization reactions. When these reactions involve the R groups of amino acids in the
enzyme structure, the change in ionic charge alters the attractive forces stabilizing the molecule, and
hence its shape and its ability to bind substrate. The specific effect of pH depends on the pKa and pKb
values of the R groups of the amino acids, especially those at the active site, and so is different for each
enzyme.
Heavy-metal ions
Heavy-metal ions cause non-competitive inhibition.
Inhibitors
competitive inhibitors bind reversibly to the active site
non-competitive inhibitors bind reversibly away from the active site
Competitive inhibitors
These block the active site making the enzyme unable to catalyse the reaction.
Increasing the concentration of substrate reduces the extent of inhibition as relatively fewer of the
inhibitor molecules are able to bind. In this type of inhibition, Vmax is not altered as there is still a
substrate concentration where full activity of the enzyme can be achieved. But as it takes a higher
substrate concentration to reach this rate, Km is increased.
Non-competitive inhibitors
The binding of this type of inhibitor causes a conformational change in
the protein structure that alters the active site, inhibiting its ability to bind
to the substrate. Increasing the concentration of substrate does not
reduce the extent of this type of inhibition as the enzymes have
effectively been decommissioned by the inhibitor and are unavailable.
Vmax is decreased and cannot be restored no matter how high the
substrate concentration. The value of Km is unchanged because the
uninhibited enzymes are perfectly functional.
B8 Nucleic acids
B.8.1 Describe the structure of nucleotides and their condensation polymers (nucleic acids or polynucleotides).
B.8.2 Distinguish between the structures of DNA and RNA.
B.8.3 Explain the double helical structure of DNA.
B.8.4 Describe the role of DNA as the repository of genetic information, and explain its role in protein synthesis.
B.8.5 Outline the steps involved in DNA profiling and state its use.
Structure of nucleotides
Nucleotides have three components:
1. A pentose (C5) sugar; in DNA it is deoxyribose (left); in RNA it is ribose (right)
2. A phosphate group PO43-
3. A nitrogenous base
A, G and C are found in both DNA and RNA, but T is only in DNA and U only in RNA.
The complete nucleotide looks like this:
Polynucleotides
The condensation reaction involves the phosphate group on 5’ and the OH group on 3’
Double helical structure of DNA
In DNA, two polynucleotide strands are coiled around the same axis forming a double helix with the
sugar–phosphate backbone on the outside and the nitrogenous bases on the inside. The two strands
are held together by hydrogen bonds that form between bases on each strand. Due to the chemistry of
the bases and the conformation of the helix, only certain base pairings involving one purine with one
pyrimidine are possible: adenine always forms a pair with thymine; guanine always forms a pair with
cytosine.
Once formed, the mRNA detaches from its DNA template and leaves the nucleus for the ribosome. The
DNA remains in the nucleus and reforms the double helix.
Translation
At the ribosome, the sequence of bases in mRNA is used to determine the sequence of amino acids in
a polypeptide. This is known as translation and involves the use of another RNA species, tRNA, which
works like an adaptor. One end of the tRNA molecule recognizes a specific triplet of bases in the mRNA
known as a codon. The other end of the tRNA recognizes a corresponding amino acid. As codons in
the mRNA are read sequentially, successive tRNA molecules bring the appropriate amino acids into
position, where they link together by peptide bonds to form a polypeptide
Hence the sequence of bases in the DNA, via RNA, determines the sequence of amino acids in the
protein. The specifi c relationship between the bases and amino acids is known as the genetic code.
As we have just seen, it is a triplet code with three bases specifying each amino acid.
DNA profiling
1. DNA is extracted
2. It is cut into small pieces using restriction enzymes. This is
because the easiest place to detect the unique nature of individual
DNA is in regions where short sequences of bases are repeated a
variable number of times. These are known as short tandem repeats
(STRs).
3. A technique known as the polymerase chain reaction (PCR) is
used to amplify these regions in the DNA by making multiple copies.
4. The DNA fragments that result are then separated and detected
using gel electrophoresis. Due to its phosphate groups, DNA carries a
negative charge. So, the fragments move towards the positive terminal
by a distance that corresponds to their molecular size: shorter
fragments move further than longer fragments. The nitrocellulose sheet
used in the electrophoresis is treated with radiation, for example 32P,
and exposed using X-ray film.
Uses
To identify victims whose bodies are not recovered from the
scene of an accident or crime.
To identify a suspect in forensic cases.
To confirm biological relationships e.g. paternity tests
To determine the relationships between populations in the study
of evolution, migration and ecology.
B9 Respiration
B.9.1 Compare aerobic and anaerobic respiration of glucose in terms of
oxidation/reduction and energy released.
B.9.2 Outline the role of copper ions in electron transport and iron ions in oxygen
transport.
Respiration
Respiration is the process of chemical breakdown of energy rich
molecules in cells with the release of energy. It takes place in all living
cells all the time. Respiration occurring in the absence of oxygen is
known as anaerobic respiration, while that using oxygen is known as
aerobic respiration.
Respiration begins with the anaerobic process of glycolysis
In glycolysis, a glucose molecule is converted into two pyruvate
molecules, C3H4O3. During glycolysis, the partial oxidation of glucose is
accompanied by the reduction of a coenzyme, a dinucleotide called
NAD+, as shown below.
The fate of pyruvate in anaerobic conditions
In order to allow the reactions of glycolysis to continue, the co-enzyme must be re-oxidised. This is
achieved by reducing the pyruvate - to lactate in human cells such as active muscles, and to ethanol
and carbon dioxide in plants or micro-organisms such as yeast.
When oxygen is present, further reactions oxidize the pyruvate in a sequence of steps which ultimately
yield carbon dioxide and water. Along the way, other reactants are successively reduced and re-
oxidized, but ultimately oxygen acts as the terminal electron acceptor and is reduced to water.
Haemoglobin
In hemoglobin and myoglobin, the uptake of oxygen is not accompanied by a change in the oxidation
number of the Fe which remains in the +2 state. Instead, the oxygen is bound in molecular form, O 2, in
the structure in a complex way that involves a conformational shift of the protein. For this reason, we
refer to these molecules as becoming oxygenated when they gain oxygen, as they are not oxidized in
the chemical sense.
Option D: Medicines and drugs
D1 Pharmaceutical products
D.1.1 List the effects of medicines and drugs on the functioning of the body.
D.1.2 Outline the stages involved in the research, development and testing of new pharmaceutical products.
D.1.3 Describe the different methods of administering drugs.
D.1.4 Discuss the terms therapeutic window, tolerance and side-effects.
Thalidomide
Thalidomide a sedative and anti-inflammatory medication and later prescribed to pregnant women in
many countries to help reduce ‘morning sickness’ in their early months of pregnancy. The drug had a
side effect on the development of the foetus leading to malformed limbs.
Administering drugs
oral – taken by mouth
inhalation – vapour breathed in; smoking; treatment of respiratory conditions
skin patches; absorbed directly from the skin into the blood e.g. nicotine patches
suppositories – inserted into the rectum; haemorrhoids
eye or ear drops – treatment of infections in those areas
parenteral (by injection)
Tolerance
When a person is given repeated doses of a drug, it sometimes happens that tolerance develops, that
is a reduced response to the drug. So higher doses are needed to produce the same effect and this
increases the chances of there being toxic side-effects.
Side effects
Side effects are physiological effects which are not intended and vary greatly from one drug to another,
and with the same drug in different people. Some side effects are beneficial e.g. aspirin, taken for pain
relief, helps protect against heart disease. Other drugs e.g. thalidomide have negative side effects.
Therapeutic window
The therapeutic window is the range of a drug’s concentration in the blood between its therapeutic level
and its toxic level. Within the therapeutic window the drug is both safe and effective.
D2 Antacids
D.2.1 State and explain how excess acidity in the stomach can be reduced by the use of different bases.
Antacids
Antacids are usually weakly basic compounds, often metal oxides or hydroxides, carbonates or
hydrogencarbonates, which react with the acid to produce a salt and water e.g.
Al(OH)3 (s) + 3HCl(aq) → AlCl3(aq) + 3H2 O(l)
Some antacids use carbonates, which produce carbon dioxide during neutralization, which can cause
stomach bloating and flatulence. To avert this antifoaming agents are added such as dimethicone.
Some antacids also contain alginates which float to the top of the stomach, forming a ‘raft’ which acts as
a barrier preventing reflux into the oesophagus (heart burn).
D3 Analgesics
D.3.1 Describe and explain the different ways that analgesics prevent pain.
D.3.2 Describe the use of derivatives of salicylic acid as mild analgesics, and compare the advantages and disadvantages of using
aspirin and paracetamol (acetaminophen).
D.3.3 Compare the structures of morphine, codeine and diamorphine (heroin, a semi-synthetic opiate).
D.3.4 Discuss the advantages and disadvantages of using morphine and its derivatives as strong analgesics.
Mild analgesics
Mild analgesics, including aspirin and non-steroidal anti-inflammatory drugs (NSAIDs) such as
ibuprofen, function by intercepting the pain stimulus at the source, often by interfering with the
production of substances (for example, prostaglandins) that cause pain, swelling or fever. They don’t
affect the function of the brain so are non-narcotics.
Strong analgesics
Strong analgesics, , work by temporarily bonding to receptor sites in the brain, preventing the
transmission of pain impulses without depressing the central nervous system. They affect the function of
the brain so are narcotics.
Salicylic acid
Salicylic acid (left) is an analgesic that comes from the bark of the willow tree. However, it tastes shit
and induces vomiting. To remedy this the OH group was replaced with an ester group and the
compound creates is aspirin (right). Aspirin has been found to be useful in preventing the recurrence of
heart attacks and strokes. The disadvantages of aspirin include ulceration and stomach bleeding,
allergic reactions and Reye’s syndrome in children (a potentially fatal liver and brain disorder).
Paracetamol is very safe in the correct dose but can, in rare cases, cause blood disorders and kidney
damage. Overdosage can lead to serious liver damage, brain damage and even death.
Aspirin Paracetamol
Side-effects stomach wall irritant, blood anti-coagulant does not irritate stomach wall
Severe side-effects (over-dosage) Reye’s syndrome in children serious kidney, liver and brain damage
Synergistic effect with alcohol increased risk of stomach bleeding toxic side-effects can be increased
Recommended use for children no; can cause Reye’s syndrome (although yes
‘baby aspirin’ is available)
Strong analgesics
Long term:
constipation
loss of libido
loss of appetite
poor nutrition
dependence
withdrawal symptoms: cold sweats and anxiety
crime
HIV and hepatitis from sharing needles
The conversion of morphine into heroin involves replacing both OH groups with less polar ester groups.
This makes heroin more lipid-soluble, so it crosses the blood-brain barrier more quickly.
D4 Depressants
D.4.1 Describe the effects of depressants.
D.4.2 Discuss the social and physiological effects of the use and abuse of ethanol.
D.4.3 Describe and explain the techniques used for the detection of ethanol in the breath, the blood and urine.
D.4.4 Describe the synergistic effects of ethanol with other drugs.
D.4.5 Identify other commonly used depressants and describe their structures.
Depressants
Depressants are drugs that act on the brain and spinal cord (known as the central nervous system or
CNS). The action of these drugs changes the communication between brain cells by altering the
concentration or the activity of chemicals called neurotransmitters. As a result they cause a
depression, or a decrease in brain activity that in turn influences the functioning of other parts of the
body, such as the heart and the mechanisms determining breathing rate.
Effects of depressants
increasing
dosage
Alcohol abuse
Short-term effects:
loss of self-restraint, concentration and insight are impaired
loss of balance and judgement
violent behaviour associated with domestic abuse and family breakdown
risk-taking behaviour
dehydration caused by increased urine output leading to ‘hangover’ and loss of productivity
at high doses, can cause vomiting, loss of consciousness, coma and death
Long-term effects:
alcoholism, withdrawal symptoms
liver diseases e.g. cirrhosis and liver cancer
coronary heart disease
high blood pressure
foetal alcohol syndrome
permanent brain damage
Detection of alcohol in breath
An equilibrium forms in the lungs between alcohol and the exhaled air. There is a specific value of KC for
a specific temperature, so measurement of alcohol in exhaled air can be used to determine the blood-
alcohol level.
Breathalyser
The breathalyser contains potassium dichromate(VI) crystals which are orange, but are changed to
green chromium(III) ions. The extent of colour change can be measured using a photocell. This test is
not very accurate.
Infrared spectroscopy
This analysis is done with an intoximeter. The principle here (Chapter 12) is that different molecules
cause different absorption bands in the infrared part of the spectrum, as a result of vibrations of their
particular bonds and functional groups. Hence ethanol has a characteristic absorption band at 2950 cm-
1 owing to its C-H bonds. The O-H bond cannot be used because it is also present in water vapour. The
size of the peak can be used to measure ethanol concentration, when compared with a reference taken
from the ambient air.
Synergy
The synergy of ethanol means it increases the activity of other drugs. Some examples are:
with aspirin, ethanol can cause increased bleeding of the stomach lining and increased risk of
ulcers
with other depressants such as barbiturates, including sleeping pills, ethanol can induce heavy
sedation, possibly leading to coma
with tobacco, ethanol appears to increase the incidence of cancers, particularly of the intestines
and liver
with many other drugs, ethanol can interfere with their metabolism by the liver, which can cause
greater and more prolonged drug effects.
Other depressants
The benzodiazepines are a major group of depressants which depress activity in the part of the brain
that controls emotion and so are used as tranquilizers in the treatment of anxiety disorders and related
insomnia. As well as being the most commonly used class of sleeping pill, they are also used as muscle
relaxants.
A widely used anti-depressant drug is fluoxetine hydrochloride, marketed as Prozac. It functions by
increasing the levels of serotonin – an important neurotransmitter in the brain. It is used in the treatment
of depression, as well as eating and panic disorders.
D5 Stimulants
D.5.1 List the physiological effects of stimulants.
D.5.2 Compare amphetamines and epinephrine (adrenaline).
D.5.3 Discuss the short- and long-term effects of nicotine consumption.
D.5.4 Describe the effects of caffeine and compare its structure with that of nicotine.
Caffeine
Note that, like nicotine, caffeine contains heterocyclic rings (containing both carbon and nitrogen) and a
tertiary amine group. In addition, caffeine contains two amide groups.
Effects of caffeine
D6 Antibacterials
D.6.1 Outline the historical development of penicillins.
D.6.2 Explain how penicillins work and discuss the effects of modifying the side-chain.
D.6.3 Discuss and explain the importance of patient compliance and the effect of penicillin overprescription.
History of penicillin
Alexander Fleming noticed that a fungus or mould known as Penicillium notatum produced a
chemical which inhibited bacterial growth.
Howard Florey and Ernst Chain isolated penicillin as the antibacterial agent.
Large-scale production methods were developed using deep fermentation tanks containing corn
steep liquor through which sterile air was forced.
Its core structure is a four-membered ring consisting of one nitrogen and three carbon atoms and known
as beta-lactam, which is responsible for the antibacterial properties. By acting as an irreversible inhibitor
of an enzyme, it prevents the development of cross-links in bacterial cell walls, so weakening the walls
and causing the bacteria to rupture and die during their reproductive phase.
Over-prescription
• Leads to greater immunity of bacteria to penicillin, since the strongest and most resistant strains
survive.
• Greater doses of penicillin are required to be effective
• Danger of developing super bacteria
• Kill beneficial bacteria as well as harmful bacteria
D7 Antivirals
D.7.1 State how viruses differ from bacteria.
D.7.2 Describe the different ways in which antiviral drugs work.
D.7.3 Discuss the difficulties associated with solving the AIDS problem.
D8 Drug action
D.8.1 Describe the importance of geometrical isomerism in drug action.
D.8.2 Discuss the importance of chirality in drug action.
D.8.3 Explain the importance of the beta-lactam ring action of penicillin.
D.8.4 Explain the increased potency of diamorphine (heroin) compared to morphine.
Geometrical isomerism
Many anti-cancer drugs function by targeting DNA to stop the division of cells. An example is cisplatin,
Pt(NH3 )2 Cl2 . It has a square planar geometry and therefore exhibits cis-trans isomerism.
In the body, the neutral complex exchanges one or both of its negative chloride groups with neutral
water ligands and so forms reactive positively charged species.
This positive species binds strongly to DNA by exchanging the water and chloride ligands for bonds
between platinum and nitrogen atoms in adjacent molecules of the base guanine (G) in the double helix.
The trans isomer cannot bond in this way so cannot be used for chemotherapy.
Chirality
When drugs are synthesised, both of the optical isomers are made. With thalidomide, one isomer
induced sleep and calmness in pregnant women and the other produced severe foetal abnormalities.
Beta-lactam ring
The bond angles in this ring are reduced to about 90°, despite the fact that, because they have sp 2 and
sp3 hybridized atomic orbitals, the atoms in the ring seek to form bonds with angles of 120° and 109.5°
respectively. This puts a strain on the bonds, effectively weakening them.
The action of these beta-lactam antibiotics is to disrupt the formation of cell walls of bacteria by
inhibiting a key bacterial enzyme, transpeptidase. As the drug approaches the enzyme, the high
reactivity of the amide group in the ring causes it to irreversibly bind near the active site of the enzyme
as the ring breaks
D9 Drug design
D.9.1 Discuss the use of a compound library in drug design.
D.9.2 Explain the use of combinatorial and parallel chemistry to synthesize new drugs.
D.9.3 Describe how computers are used in drug design.
D.9.4 Discuss how the polarity of a molecule can be modified to increase its aqueous solubility and how this facilitates its
distribution around the body.
D.9.5 Describe the use of chiral auxiliari
The first step in developing a drug is to identify the molecular target; this is usually an enzyme, a
receptor or DNA.
Combinatorial chemistry
Combinatorial chemistry is a process used to synthesize a large number of compounds, called
combinatorial libraries. The reactions involved usually occur on insoluble resin beads, a technique
known as solid-phase chemistry.
Different molecules can be made using the mix and split method:
Subsequent screening of the products for the desired activity will hopefully identify a useful lead
compound
The IB mark scheme gives the following as acceptable answers to the question explain what is meant
by combinatorial chemistry:
Any three of the following.
process used to synthesize a large number of compounds / OWTTE;
compounds are structurally related;
repetitive/computerized technique;
screen them for biological activity / OWTTE;
produces a library/database of different compounds / OWTTE;
Parallel synthesis
Parallel synthesis produces libraries that are more focused and less diverse than those from
combinatorial techniques. Parallel synthesis usually involves the synthesis of a highly reactive
intermediate via a series of simple steps, then its subsequent reactions with a number of different
reagents. One of the popular means of achieving this is known as the teabag procedure in which
porous bags of resins are suspended in reagents. Automated or semi-automated synthesizers can yield
up to 144 structures in separate reaction tubes.
Computer-aided design
Three-dimensional models of drugs can be created in silico and molecular modelling software can be
used for the virtual development and evaluation of new drugs. Molecular-modelling software analyses
the interaction between the drug and its receptor site, helping to design molecules that give an optimal
fit. The part of the drug molecule that permits the specifi c binding and is responsible for the activity is
called the pharmacophore. Even when the exact structure of the receptor site is not known, a process
called pharmacophore mapping can derive a model called a 3-D pharmacophore. This is done by
analysing the molecules that bind to the receptor, searching for their common features and using
software to predict the most likely three-dimensional structure. Computers should reduce the number of
candidate molecules that must be tested, and means fewer molecules have to be tested in vivo (in living
organisms).
Chiral auxiliary
A chiral auxiliary is used to convert a non-chiral molecule into just the desired enantiomer, thus avoiding
the need to separate enantiomers from a racemic mixture. This is a chiral molecule which binds to the
reactant, physically blocking one reaction site through steric hindrance, so ensuring that the next step in
the reaction can only take place from one side. This effectively forces the reaction to proceed with a
specified stereochemistry. Once the specific enantiomer of the new product has been set, the auxiliary
can be taken off and recycled.
Legalisation of cannabis
Arguments for legalization include the ability of cannabis to offer relief from certain diseases.
Arguments against legalization include the possible harmful effects and the possibility of
cannabis users moving on to harder drugs.