X-ray diffraction

• The atomic structure of crystals cannot be

determined by optical microscopy because the
wavelength of the photons is much too long (400 nm
or so).
• So one might want to build an x-ray microscope but
this does not work for very small wavelength
because there are no suitable x-ray optical lenses.
• The idea is to use the diffraction of x-rays by a
perfect crystal.
• Here: monochromatic x-rays, elastic scattering,
kinematic approximation

1
 X-rays
• X-rays are produced when electrons are accelerated and collide with a
target
• An electrically heated filament, usually tungsten, emits electrons, which
are accelerated by a high potential difference (20–50 kV) and allowed to
strike a metal target or anode which is water cooled
• The anode emits a continuous spectrum of ‘white’ X-radiation

– Bremsstrahlung x-rays
– Characteristic x-rays
• X-rays are sometimes characterized by the generating voltage
– 0.1-20 kV soft x-rays
– 20-120 kV diagnostic x-rays
– 120-300 kV orthovoltage x-rays
– 300 kV – 1 MV intermediate energy x-rays
– > 1MV megavoltage x-rays

2
 Characteristic x-rays
• After excitation, ions
with a vacancy in their
inner shell can de-
excite
– Radiatively through x-
ray fluorescence
– Non-radiatively
through the emission
of Auger electrons

3
 Characteristic X-rays
• Thus an x-ray spectrum will also show
characteristic x-rays arising from L to K and M to K
transitions after ionization of a K electron
– Usually transitions to higher shells absorbed by
the filtration or are not x-rays

4
Characteristic X-rays

Decelerating charges give off radiation

Characteristic X-rays
 X-ray Tube

• A simplified x-ray tube (Coolidge type) shows

the idea behind most x-ray tubes today

7
 Properties of X-rays

• X-rays travel in straight lines.

• X-rays cannot be deflected by electric field or
magnetic field.
• X-rays have a high penetrating power.
• Photographic film is blackened by X-rays.
• Fluorescent materials glow when X-rays are
directed at them.
• Photoelectric emission can be produced by X-rays.
• Ionization of a gas results when an X-ray beam is
passed through it.
 X-ray Tube

• More detail

9
 X-ray Tube

• The main parts of the x-ray tube are

– Cathode/filament
• Typical electron current is 0.1-1.0 A for short exposures
(< 100 ms)
– Anode/target
– Glass/metal envelope
– Accelerating voltage
• Typical voltage is 20-150 kVp

10
 Cathode
• Cathode consists of
– Low R tungsten wire for thermionic emission
• Tungsten has a high melting point (3370C) and minimum deposit
on the glass tube
• Tube current is controlled by varying the filament current which is
a few amps
– A focusing cup
• Uses electric field lines to focus the electrons
• Typically there are two filaments
– Long one: higher current, lower resolution
• Large focal spot
– Short one: lower current, higher resolution
• Small focal spot

11
Anodes
common - Cu, Mo, Fe, Cr, W, Ag
• The crystals can be used to diffract X-rays (von Laue,
1912). X-ray diffraction

13
The Bragg description (1912): specular reflection

and this only works for

• The Bragg condition for constructive interference

holds14 for any number of layers, not only two (why?)
 X-ray diffraction: the Bragg description
• The X-rays penetrate deeply and many layers
contribute to the reflected intensity
• The diffracted peak intensities are therefore very
sharp (in angle)
• The physics of the lattice planes is totally
obscure!

15
 What is Bragg’s Law?
• Bragg's Law refers to the simple equation:
nλ = 2d sinΘ
derived by the English physicists Sir W.H. Bragg and his son Sir
W.L. Bragg in 1913 to explain why the cleavage faces of crystals
appear to reflect X-ray beams at certain angles of incidence (Θ,
λ).

• The variable d is the distance between atomic layers in a

crystal, and the variable lambda is the wavelength of the
incident X-ray beam (see applet); n is an integer.

• This observation is an example of X-ray wave interference

(Roentgenstrahlinterferenzen), commonly known as X-ray
diffraction (XRD), and was direct evidence for the periodic
atomic structure of crystals postulated for several centuries.
 What is Bragg’s Law?
• The Braggs were awarded the Nobel Prize in physics
in 1915 for their work in determining crystal structures
beginning with NaCl, ZnS and diamond.

• Although Bragg's law was used to explain the

interference pattern of X-rays scattered by crystals,
diffraction has been developed to study the structure
of all states of matter with any beam

• E.g., ions, electrons, neutrons, and protons, with a

wavelength similar to the distance between the atomic
or molecular structures of interest.
 Deriving Bragg’s Law
Fig. 1 Deriving Bragg's Law using the reflection
geometry and applying trigonometry. The
lower beam must travel the extra distance (AB
+ BC) to continue traveling parallel and
adjacent to the top beam.
Bragg's Law can easily be derived by
considering the conditions necessary to
make the phases of the beams coincide
when the incident angle equals and
reflecting angle. The rays of the incident
beam are always in phase and parallel up to
the point at which the top beam strikes the
top layer at atom z (Fig. 1). The second
beam continues to the next layer where it is
scattered by atom B. The second beam must
travel the extra distance AB + BC if the two
beams are to continue traveling adjacent
and parallel. This extra distance must be an
integral (n) multiple of the wavelength (λ)
for the phases of the two beams to be the
same:
nλ = AB +BC (2).
 Deriving Bragg’s Law (cont.)
Recognizing d as the hypotenus of the right
triangle Abz, we can use trigonometry to relate
d and Θ to the distance (AB + BC). The distance
AB is opposite Θ so,

AB = d sinΘ(3).

Because AB = BC eq. (2) becomes,

nλ = 2AB (4)

Substituting eq. (3) in eq. (4) we have,

nλ = 2 d sinΘ, (1)

and Bragg's Law has been derived. The location

of the surface does not change the derivation
of Bragg's Law.
Experimental Diffraction Patterns
This figure shows an experimental x-ray diffraction pattern of cubic
SiC using synchrotron radiation.
UNIT CELL TYPES and THE SEVEN CRYSTAL SYSTEMS
Cubic a = b = c.  =  =  = 90º.
Tetragonal a = b  c.  =  =  = 90º. c b
Orthorhombic a  b  c.  =  =  = 90 º.
Monoclinic a  b  c.  = = 90º,   90º. a
Triclinic a  b  c..       90º. Orthorhombic
Rhombohedral a = b = c.  =  =   90 º.
(or Trigonal)
Hexagonal a = b  c.  =  = 90º,  = 120º.

In general, six parameters are required to define the shape and size of a unit cell,
these being three cell edge lengths (conventionally, defined as a, b, and c),
and three angles (conventionally, defined as , , and ). In the strict mathematical
sense, a, b, and c are vectors since they specify both length and direction.
 is the angle between b and c,  is the angle between a and c,  is the angle
between a and b. The unit cell should be right handed. Check the cell above with your right
hand
When these unit cells are combined with possible “centering” there are
14 different Bravais lattices.

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Cubic

Tetragonal

Orthorhombic

Body Face
Monoclinic
Centred Centred
Cell Cell
I F

Triclinic End Face Centred

Cell
C

Trigonal

Hexagonal

Primitive Cell
P

The 14 Bravais Lattice system

 Selection / Extinction Rules
 As we have noted before even if Bragg’s equation is satisfied, ‘reflections may go missing’
 this is due to the presence of additional atoms in the unit cell.
 The reflections present and the missing reflections due to additional atoms in the unit cell are
listed in the table below. Click here to see the derivations
Structure factor calculations

Bravais Lattice Reflections which may be present Reflections necessarily absent

Simple/ Primitive all None
Body centred (h + k + l) even (h + k + l) odd
Face centred h, k and l unmixed h, k and l mixed

End centred (C centred) h and k unmixed h and k mixed

Bravais Lattice Allowed Reflections

SC/P All
BCC/I (h + k + l) even
FCC/F h, k and l unmixed
Either,  h, k and l are all odd or
C
 all are even & (h + k + l) divisible by 4
 h2 + k2 + l2 SC/P FCC/F BCC/I C
1 100
Allowed reflections 2 110 110
in P*, F*, I* & C 3 111 111 111
crystals 4 200 200 200
5 210
6 211 211
7
8 220 220 220 220
Cannot be expressed as (h2+k2+l2) 9 300, 221
10 310 310
11 311 311 311
12 222 222 222
13 320
14 321 321
15
16 400 400 400 400
17 410, 322
* lattice decorated with 18 411, 330 411, 330
monoatomic/monoionic
motif 19 331 331 331
 Basis and Bravais Structure Factor Terms
Np Nb
F  e 2  igrn
m
f e 2  igrm
 FBR FBA
n1 m 1
The following simple table giving the integer values of FBR for the different types of centering
translations. Keep in mind that these are valid for any crystal system.

Centering type Missing Reflections Possible Reflections Bravais Term FBR for
(FBR = 0) (FBR ° 0) possible reflections
P (primitive) None All 1
I (body-centered) (h + k + l) odd (h + k + l) even 2
A (base-centered on A (k + l) odd (k + l) even 2
face)
B (base-centered on B (h + l) odd (h + l) even 2
face)
C (base-centered on C (h + k) odd (h + k) even 2
face)
F (face-centered) hkl mixed hkl unmixed 4
Crystallite size
SOLVING A CRYSTAL STRUCTURE BY SELECT A SUITABLE
CRYSTAL
SINGLE CRYSTAL DIFFRACTION TECHNIQUES A
N.B. The crystal must be a single crystal.
CRYSTAL SYSTEM
and
UNIT CELL DIMENSIONS
Bragg's equation specifies that, if a crystal is rotated
B
within a monochromatic X-ray beam, such that every
conceivable orientation of the crystal relative to the beam FULL DATA SET
COLLECTION
is achieved, each set of planes will have had the
C
opportunity to satisfy the Bragg equation and will have
BRAVAIS LATTICE
given rise to reflection.
In order to solve a crystal structure it is necessary D

to record a large number of reflections. SPACE GROUP

This implies accurately measuring their intensities and E

recording their directions with respect to crystal orientation CONSTRUCT AN

and initial X-ray beam direction. ELECTRON DENSITY
MAP
Many experimental techniques have been devised F
to achieve this. The steps involved in a crystal structure
LOCATE ATOM
determination are summarised in the flow chart. POSITIONS
G

STRUCTURE
REFINEMENT
 Diagram Of An Area Detector X-Ray Data Collection System.
Image Plate / CCD
The first crystallographic
data collection systems used Diffracted Beam & Spot

photographic methods. These

were replaced by automated
diffractometers which measured
reflections one at a time. A typical Crystal
Beam Stop


data collection took several days.
modern systems use area detectors
which measure 100s at a time. X-ray Beam

The crystal is oscillated over < 2°

while an image is collected then
rotated by the same amount
and oscillated again. The process is
repeated over a total range of about 180°.
Each image is exposed for < 100s.
Thus if readout time is ignored total
data collection time is often < 3 hr.
A typical image shown to the left.
A computer program is used to predict
the unit cell from several images.
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 Determination of the Lattice type and Space Group

High symmetry can lead to reflections being systematically absent from the
data set. Absent reflections have no measurable intensity. There are two types
of absences, General Absences and Special Absences.
The general absences determine the lattice type;
Primitive (P) has no general absences and no restrictions on h, k or l.
End Cantered (C) h+k=2n+1 are all absent.
Face Cantered (F) only h, k, l, all even or all odd are observed.
Body Cantered (I) h+k+l=2n+1 are all absent.

The special absences refer to specific sets of reflections and are used to
detect the presence of glide planes and screw axes. Some Space Groups
are uniquely determined by special absences but in many cases several
Space Groups will have to be considered.

Computer programs are able to lay out the data in tables with absences
indicated and possible Space Groups can be suggested however the choice of
Space Group will often need much thought.
 Solving the Structure

There are two ways to solve the phase problem:

1. The Patterson or heavy atom method

2. Direct Methods (Hauptman and Karle 1985 Nobel prize)

2. The Charge flipping method is a recent development

 The Patterson or heavy atom method.
It is the electrons that scatter X-rays. Atoms that are heavier than all others
in the crystal will give rise to the strongest reflections. Heavy is a relative term
however, all atoms after Rb are normally considered to be heavy.
Iodine for example will scatter a lot of X-rays compared to carbon. Using the
Patterson method it should be possible to calculate the position of an iodine
atom and this could be used to phase most of the reflections and calculate
an electron density map.
Direct Methods
After many years of study statistical trends were observed in reflection phases.
It was also observed that some reflections are more important than others.
The Direct Methods approach tries to guess the reflection phases and then
awards a Figure of Merit to the guess. The most popular is the Combined Figure
of Merit or CFOM). It is normal practice to accept solutions with CFOM values
in the range 0.03-0.15 and to try to use these phases to generate an
electron density map.

Charge Flipping
The charge flipping method works well if the data has good resolution.
There is an example in the Oscail tutorials. All non-H atoms are often identified
correctly in the solution.
 Refining a Structure
It should be possible to “see” atoms in an electron density map if it has good
resolution i.e. at least 1Å resolution. The steps in refining a structure are.
1. Use whatever atoms you have that look OK to generate an electron density
map.
2. The known atoms are subtracted from this to generate a difference map.
3. Any atoms that have been missed should be in the difference map.
4. The refinement process minimises the difference between observed and
calculated reflection intensities.
5. In the final difference map there should be no peaks larger than a H atom
i.e. > 1e/Å3. (A H atom has a volume of about 1Å3 and has 1 e.)

Resolution The resolution of a crystal structure is usually quoted in Angstroms, Å.

Standard small molecule structures should always be at least
of 1 Å resolution to give accurate bond lengths. Resolution can be related to Bragg
angle at any wavelength through the Bragg equation n = 2d sin. Using the  value
of the reflection with the largest Bragg angle in a data set
then d = /2sin gives the resolution. The pattern shown on slide 15 has a
resolution of 0.98Å at the edge.
 Final stages of refinement.
There are many was in which a structure can be “improved”. The two most
important considerations are addition of hydrogen atoms and anisotropic
refinement of the non-hydrogen atoms.

Addition of hydrogen atoms – Hydrogen atoms have only 1 electron and are
often not seen in difference maps. It is best to include them at calculated
positions. This is easy to do and it will improve the “R factor”.
Anisotropic refinement of the non-hydrogen atoms – In the early stages
atoms are refined as if they were spheres. Since atoms vibrate in a way that
is controlled by chemical bonds and interactions with their neighbours,
it is better to refine then as ellipsoids. One parameter (the radius) is enough
to define a sphere this with x,y,z means that isotropic refinement requires
4 parameters per atom. An ellipsoid needs 6 parameters thus an anisotropic
atom requires 9 parameters.
This is an example of an anisotropic atom

R Factor – The R factors used are Rw and wR2. Rw should be < 8% and
wR2 should be <15%. The lower the better. If the R or error is greater then
these values the structure is not much use. Rs are of the form Sum[(I0-Ic)/Io]
 Powder- X-ray Diffraction (p-XRD)
•The pXRD is a method to characterize the
crystallographic structures by analysing their
diffraction pattern.

•It is a rapid, non-destructive method used for the

identification, purity and phase of a crystalline
material.

•This is possible because each crystalline solid has

its own unique characteristic X-ray powder
diffraction pattern which can be used as a
‘fingerprint’ to identify it.
 Powder- X-ray Diffraction (p-XRD)

• Monochromicatic X-rays, with a wavelength λ,

are projected onto a sample, at an angle of θ,
and this causes secondary diffracted beams of
X-rays in the form of cones.
• X-rays which are reflected from the surface
travel a shorter distance than those which
penetrate into the internal layers of the
sample.
 Powder- X-ray Diffraction (p-XRD)
• The distance travelled by the X-ray depends on the angle at
which the X-ray entered and the separation of the layers.

• For this wave to be in the same phase as the wavelength

which was reflected from the surface it needs to have
travelled a whole number (n) of wavelengths whilst inside the
material thus leading to constructive interference.

• This means the greater the number of wavelengths in phase

the greater the intensity.

• If the distance is not an integral number then deconstructive

interference occurs and the reflected wavelength is not
detected .
 Powder- X-ray Diffraction (p-XRD)
•These diffracted rays (2θ) are converted to d-spacings
which are then matched with standard reference patterns
stored in the ICDD (International Centre for Diffraction Data)
database.
•An X-ray diffractometer is comprised principally of an X-ray
tube, a sample holder and an X-ray detector/monitor.
Powder- X-ray Diffraction (p-XRD)
•Typical anode materials include Cu (most
common), Co, Mo, Fe and Cr.

Schematic of X-ray diffractometer