Introduction to

crystal
structures
and X-ray
diffraction
Session (1)
Why are Crystal Structures relevant to Chemical Engineering?

Catalysis: Crystals at the heart of the chemical industry

Processes in the chemical industry Catalytic processes
Heterogeneous
catalysis
All processes 80%

Catalytic processes
85%

Homogeneous
catalysis
17%
Biocatalysis
3%

Non-catalytic
processes
15%
Pt3Co nanoparticle catalysts:

- Candidates for oxygen reduction

reaction in fuel cells

- Metal nanoparticle catalysts are

ubiquitous including in catalytic
converters (cars) and throughout the
chemical industries

- Here, atomic resolution images of

bimetallic nanocrystals are shown at
different processing temperatures
(annealing temperatures) to track
changes in the structures at the exposed,
active catalytic surface
 Zeolite Frameworks from Sodalite Cages

(a)Sodalite (or β-) cage;

(b) zeolite A, the β-cages are linked to each other via double four-membered rings (O
bridges)

(c) zeolite Y, the β-cages are connected via double six-membered rings (O bridges)
 Applications of Zeolites
• Distinctive Crystal Structure gives distinctive properties
Molecular Sieve
• small molecules can be separated from larger molecules (gas or liquid)
• filtration by size exclusion
Sorbent Material
• High surface area due to microporous structure
Water Softening
• Na+ in pores: ion exchange for Ca2+, Mg2+ ions in water
Catalyst (including hydrocarbon cracking)
• Pores act as locations for catalytic reactions
• Acidic sites (Lewis Acid; Bronsted acid)
 Aluminosilicates
- Clays (e.g. kaolinite)
- Uses in ceramics
- Porcelain and similar products
- SiO4 Tetrahedra
- AlO6 Octahedra
- Layered network

- Similar aluminosilicate arrangements in

zeolites, minerals, and ceramics
 Metal–organic frameworks (MOFs)
- Exceptional porosity (surface areas >7000 m2/g
achieved compared to ~300-500 m2/g for many
common zeolites)

- Use molecular and coordination chemistry principles to

achieve repeating pore structures for applications in gas
NuMat technologies: ​ storage, chemical separations, water purification,
Phosphine gas cylinders at carbon dioxide sequestration (carbon capture) and
lower pressure​ catalysis.

- High cost (complex ligand synthesis, transition metals),

challenges in scale-up for commercial production

- Commercialization example: Targets high value

semiconductor fabrication where safety considerations
outweigh production costs
Industrial Crystallisation
Tetrahedra

Knowledge of crystal structures helps

to understand and control shape and
properties of crystalline particles
(see notes on crystal planes and Miller Cubes
indices)

e.g.:
• Reactivity (rate of conversion) ‘Near
• Chemical selectivity (which spherical’

products)
• Solubility
Model system: electron transfer reaction between
• Particle size and particle packing hexacyanoferrate (III) and thiosulfate ions
Practical Examples of
Knowledge of Crystal
Structures:

Understanding the
shape of particles

9
Small Batch Hydrothermal Reactor
Shape of Particles Produced in Hydrothermal Reactor
• External morphology reflects crystal structure (hexagonal unit cell)

• Lowest energy lattice planes develop

{10-10} (0001) ZnO:

hexagonal
unit cell

<0001>
 Piezoelectric Ceramics
• Sonar

• Non-destructive testing

• Imaging contents of reaction vessels

 Fuel Cells
• Solid oxide Fuel Cell

• Generates electricity from oxygen and hydrogen

• (or methane, methanol)

• Solid electrolyte: separates fuel from oxygen and allows O 2- to pass

• Crystal structure of solid electrolyte is key

Solid Oxide Fuel Cell

• O2- ions pass through solid

electrolyte

• ZrO2 crystal structure

allows O2- ions to migrate
 Polymorphism
• Materials can crystallise with their molecules with different intermolecular arrangements called
polymorphs
• This is particularly common in organic materials such as pharmaceutical materials
• These different arrangements impact upon the physical properties of the material, such as morphology

Example: para-aminobenzoic acid

• Used in biomedical synthesis and dyes
• Two well-known polymorphs α and β

PA BA
α-
Molecules stack efficiently resulting
in needle crystal morphology Anisotropic
needle
β -P
AB
A

Isotropic
Molecules arrange in a ring like structure prismatic plate
resulting in a prismatic morphology 15
The lattice, periodicity and crystal
structures
Lattice:
An infinitely extended periodic set of points (geometric
concept)

Crystal:
An infinitely* extended periodic array of atoms defined on a
lattice
*Theoretically
2D Lattice: Possible choices of the repeating unit
All points identical and identically separated (square lattice):
1D repeating units Where do each of the following = ‘One’
sequences of dots repeat? = ‘And’
(Alternatively: consider each as a
word/sound) = ‘ah’
1D repeating units
Assume a function of the type:

Wavelength
λ

(Length
increased 10x)
In general:

x=0 x=d
1
𝑘=
𝑑
Periodicity in solids: repetition in space

In 2D

The wavevector:
k points in the direction of the repeat,
where wave comes back to same value In 3D
(the wavefront)
Close packing and voids
(Lawrence Bragg)
 Metal Crystal Structures
• Atoms pack together (hard spheres) to maximise space filling
• Each layer of ping-pong balls represents a layer of close packed metal
atoms
• Scale ~ billion to one
• Teaches basics of packing, and highlights void spaces
Ping-pong ball models

Commercial crystal models

Computer software to make 3D diagrams of crystals

X-ray diffraction to study basics of crystal structure

 Building Models of Metal Crystal Structures

First consider,
- one layer of atoms

- two layers of atoms

void spaces between layers

tetrahedral voids
octahedral voids
 One layer of Close Packing (CP)

Maximum Space Filling. Each atom surrounded by 6 other touching atoms. Spaces
(Voids) formed by 3 touching atoms
 Voids in Atom Close Packing
Consider two layers of spheres.
Place a second layer on top of the first.
Ensure the spheres of the upper layer nestle into the depressions of the first to
maximise space-filling.
Observe the spaces between the layers
Hint: repeatedly separate them slightly and slowly bring them together,
observing the spaces that are enclosed by groups of spheres between different
layers.

You should see two different types of void space.

 Two Close Packed (CP) Layers
Bottom layer

Top Layer
T-

T+
O

T = Tetrahedral void (T+ & T - indicate inverted tetrahedra)

O = Octahedral Void
 Two CP Layers
Bottom Layer A
Layer

Top
Layer
Layer B
 Tetrahedral Voids
4-touching atoms
This type of void is formed when the gap between 3 touching spheres in
one layer lies immediately above/below a sphere from an adjacent atom
layer.

Try to sketch a plan view, looking from above, of a group of 4 touching

spheres that enclose a tetrahedral void.
Hint: use a coin to draw a circular projection and use a dashed line to
represent a sphere in the bottom layer and a solid line for the upper layer
spheres.
 Tetrahedral Voids
By looking at your diagram, and the models, convince yourself that the
centres of the spheres which enclose this void lie at the corners of a regular
tetrahedron
- hence the name Tetrahedral Void

A tetrahedron formed from 4 touching spheres

plan view perpendicular to CP layers
 Tetrahedral Void
2 4
1
4
1
2
4
2

3 3

Plan View Perspective View

Atoms 1, 2, 3 in same CP layer Regular tetrahedron formed from
Atom 4 in CP layer above centres of touching spheres
 Two types of Tetrahedral Void
2
2 1
1

4
4

3 3
T+ T-

Atom 4 in Atom 4 in layer

layer above below
 4

Octahedral Void 1 2

• The other type of void in the two-

layer sandwich is an Octahedral Void.
5 6

• Octahedral void is formed between 3 3

touching atoms in one CP layer and 3
in a second layer Plan View of Octahedral void
perpendicular to CP layer

• When viewed perpendicular to the Atoms 1,2,3 in one CP layer

close packed layers, the central Atoms 4,5,6 in CP layer above
portion of this type of void is visible.
 Octahedral Void
4

1 2

5 6

Octahedron lying on a face

Blue atoms 1,2,3 in bottom CP Regular Octahedron
Clear atoms, 4,5,6 in top CP layer
Inset ‘regular’ perspective
view of octahedron
Views of an Octahedron

View along arrowed

direction
Octahedral Void
Cubic and hexagonal
close packing
 Three Close Packed Layers
ABA stacking Sequence 1st and 3rd layers coincide (A layers)

Layer 1

Layer 2

Can see through

structure:
columns of
octahedral voids
 Hexagonal Close Packing HCP

• ABABABA----- atom CP layer stacking sequence is termed:

Hexagonal Close Packing (HCP)
'ABA' or 'AB' stacking

• Many metals have this crystal structure e.g., Titanium at room

temperature
 Visualisation in Crystal Maker
HCP
 Three Close Packed Layers
ABC stacking Sequence 3rd layer atoms lie directly above octahedral voids (layers 1 & 2)

C Cannot see
through structure
(contrast to ABA)
 Cubic Close Packing CCP
• ABCABCABC----- atom CP layer sequence is termed:
Cubic Close Packing (CCP)
'ABC' stacking repeat

• This is also a common metal structure

e.g., Copper
CCP 3

2
1
1 2 3 1 2 3

If all atoms in a single layer are in contact with each other (close packed), then the void
space in two-dimensions is described by an equilateral triangle. When the atoms repeat
across the layer, this forms an arrangement where each atom is in contact with six. The
‘pizza slice’ shown on the left can be rotated 6 times to fill in this pattern.

As we see in the HCP structure (plan view), the feature that we can tile (slide and repeat) is a
diamond consisting of two end-to-end (or equivalently side-to-side) equilateral triangles.
CCP

A-B-C

Seeing the close packed layers in CCP can be challenging. I have here colour-coded the atoms in the A-B-C
layers and represented the set with an expanded number of atoms in a plan view or, equivalently, a top-down
view. The expanded set of atoms come from adjacent unit cells – these are not the same atoms shown on the
left but show how the sequence of layers form the A-B-C stack. Consider moving the colour-coded layers to
expand or re-arrange the ‘pizza’ slices on the right to see how the extended repeating packing within the
layers matches up with the representation on the left.
Visualisation in CrystalMaker
CCP
 Common Points Regarding HCP and CCP
• Co-ordination number = 12
each atom is surrounded by 12 nearest- neighbour atoms
1 octahedral void per atom
2 tetrahedral voids per atom
Twice as many tetrahedral voids as octahedral voids
(voids also called interstices)
 ‘Size’ of octahedral & tetrahedral voids
• Can calculate the maximum diameter of smaller atom which would just fit
inside an octahedral void (see worked examples on Minerva)
• In terms of r, the radius of the CP atoms

‘Size’ of an octahedral void = 0.414 r

‘Size’ of tetrahedral void = 0.225 r

Try calculation yourself for a triangular void in one layer of CP atoms (0.155r)
• 0.414 r and 0.225 r can be thought of as the radius ratio of atoms just
fitting inside octahedral (Oh) and tetrahedral (Td) voids respectively
Hint to Approach to Calculate Void Size
Pythagorean Theorem

a2 + b 2 = c 2
c is the hypotenuse of a right-angled triangle
c
a

50
 Triangular Void in 1 CP Layer
Edge of equilateral triangle = 2r

Red = radius of small atom inside void

CP atom radius r h
r
Work with this half of
equilateral triangle
2r
h r

2r
 Triangular Void in 1 CP Layer
• Use Pythagoras
Edge of equilateral triangle = 2r

Red = radius of small atom inside void

CP atom radius r

r Work with this half of

equilateral triangle
2r
h r

2r
Centre of void = centre of equilateral triangle
( which lies 1/3h from base)
[(Distance from centre to corner) – 1r] = Answer
 Apply Pythagorean theorem

• a2 + b2 = c2
h
r

2r

h2 + r2 = 4r2

h2 = 3r2
h = (√3)r
 h s s h
r

2r
(1) Can you use Pythagoras to solve
for h in terms of r?
30° 30°
r r
(2) Can you use this additional (3) How does s relate to h when both
triangle to work out the length s are written in terms of r?
in terms of r?

h2 + r2 = (2r)2
h2 + r2 = 4r2
h2 = 3r2
 Triangular Void in 1 CP Layer
• Use Pythagoras Centre of void lies (1/3)h from base

And lies (2/3)h from corner atom’s centre

h
CP atom radius r 1/3
h
2/3 Work with this half of
equilateral triangle
2r
h = (√3)r
Same principles
can be applied to
tetrahedral and Centre of void lies at centre of equilateral triangle
octahedral void max size of sphere in void space =
size calculations. [(Distance from centre of equilateral triangle to corner) – 1r]
= [(2/3)(√3)r – 1r] = 0.155r. ‘Size’ of triangular void
 Tetrahedral and octahedral void sizes
• Identify location of void centre within the Td or Oh

• Remember CP atom centres form corners of the Td or Oh structure

• Calculate distance from void centre to a corner

• Subtract the radius of the CP atom

• This gives the radius of atom just fitting void

• Touches surface of CP atom
Unit cells
Unit Cell of a Crystal

Definition of Unit Cell

Smallest repeating unit of the
crystal structure that represents the
symmetry of the structure
 Unit Cell: Example 2D Pattern of Circles
Lattice parameter 2 = Lattice parameter 1 = a

Lattice parameter 1

constant Unit Cell

Motif
Isolated Unit Cell
 Unit Cell- one circle per unit cell
Each circle (motif) shared by 4 adjacent unit cells
0.25 of each circle lies within this unit cell

Each of the 4
corners
contributes 0.25
of a circle to this
unit cell.

Hence there is 1
circle (4 x 0.25)
per unit cell in the
extended pattern.

‘ the sharing factor is ¼’

Generating the Pattern by
Repeating the Unit Cell
Patterns and Unit Cells

Unit Cell
 Unit Cell of CCP
view showing centres of atoms

4 atoms per unit cell

See next slide for

full scale atoms
Unit Cell CCP- space filling

Atoms touch diameter-diameter along face diagonal

 CCP Unit Cell - description
• Atom located at each corner and at each face centre of a cubic cell

• Face Cantered Cubic (FCC) – a Bravais Lattice*

• CCP is the crystal structure

Note: FCC refers to shape of Unit Cell (cubic) and distribution of lattice
points (face cantered)*.

• ‘CCP has a FCC structure’ or ‘FCC Packing’ are loose descriptions

Unit Cell of CCP-
Usual Diagram of Unit Cell CCP
 Unit Cell dimensions
• Copper CCP unit cell (at 20 °C)
Lattice parameter or
3.16 x 10-10 m cube edge-length
lattice constant
• 3.16 Angstroms, 3.16 Å (1Å = 1 x 10-10 m).

• 316 pm (1 pm = 1 x10-12 m)

• All Angles = 90 °
 Unit Cell CCP- space filling

Body diagonal highlighted (line between diagonally opposite corners)

Unit Cell of CCP-
view showing centres of atoms
A body
diagonal
Unit Cell CCP – view along body diagonal
3-fold axis of rotation

Rotate every 360/3 degrees (120 degrees) - replicate image

Unit Cell of CCP-
view showing centres of atoms- highlight one set CP layers

CP planes at
right angles
to body
diagonals
Unit Cell of CCP-
view showing centres of atoms

Further
set of CP
planes

Cube has 4 body diagonals: Set of CP planes lies at right angles

to each body diagonal. Total = 4 sets of CP planes.
Unit Cell CCP–view normal to face
4-fold axis of rotation

Face
diagonals
highlighted

Replicate image every 360/4 degrees

Packing density
Unit Cell CCP- space filling

Atoms touch along face diagonal in manner shown

Calculation of CCP Packing Density
Step 1

• Calculate number of atoms per CCP unit cell

• Remember sharing factor)

• Consider radius of CP atom = r

(continued)
Step 2

• Calculate total volume of atoms per cell

• Atom is a sphere

• Vol of one sphere = 4/3 π r3

Consider number of atoms per cell. In CCP 4 atoms /cell

4 atoms/cell
Tot Vol. atoms = 4x(4/3πr3)
3
Step 3 Calculate Vol Unit Cell

Edge = 1 /√2 . (Face diagonal)

√2
1
1

We know that face diagonal = 4r in CCP

Edge = 1 /√2 . (4r) = 2.828 r
Step 3. Calculate Vol of Unit Cell

Edge length of Cube

(1 / √2) x face diagonal
(1 / √2) x 4r
= 2.828 r.
√2
1
1

Vol. cell = (2.828r)3 = 22.62 r3

Packing Density CCP

Packing Density = (volume atoms)/(volume cell)

Packing Density = 16.755r3 / 22.62 r3

= 0.74 or 74%

Maximum space filling achievable by equal sized spheres

Thank
You