Structure Factors & Fourier

Transforms
How to get more than unit cell sizes from your diffraction data

Chem 4850/6850/8850
X-ray Crystallography
The University of Toledo

http://homepages.utoledo.edu/clind/
Yet again… expanding convenient concepts
 First concept introduced: Reflection from lattice planes
- facilitates derivation of Bragg’s law
- explains the location of spots on the observed diffraction pattern

 Second concept introduced: Scattering from atoms, all the

electron density was assumed to be concentrated in a “lattice
point” (e.g., origin of the unit cell)
- gave the correct locations for spots in the diffraction pattern

 But what about atoms that are located “between lattice planes”?
- any atom can scatter an X-ray that hits it
- what does this imply for the overall scattering amplitude?
 Atoms “between lattice planes”
 “Atoms between lattice planes” will always scatter X-rays so
that the resulting wave is partially out of phase with X-rays
scattered from the “lattice planes”
- the “lattice planes” can be envisioned as atoms located in the plane
described

“Structure Determination by X-ray Crystallography”,

Ladd and Palmer, Plenum, 1994.
 Description of a plane
 Point P can be described by the
vector p, which is perpendicular
to the plane LMN, or by the
coordinates (X,Y,Z)
- the intercept equation of the plane
is given by
X/ap+Y/bp+Z/cp = 1
- this can be rearranged to
“Structure Determination by X-ray Crystallography”,
Ladd and Palmer, Plenum, 1994.
X cos + Y cos + Z cos = p

- describes family of parallel planes that are located at distance |p| from 0
 Path difference
X cos + Y cos + Z cos = p

For plane O’: p = dhkl; ap = a/h; bp = b/k; cp = c/l

cos = dhkl/(a/h); cos = dhkl/(b/k); cos = dhkl/(c/l)

For plane A: pA = dA; atom at (XA, YA, ZA)

d d d
⇒ d = X ⋅ hkl + Y ⋅ hkl + Z ⋅ hkl
a/h b/k c/l

d = (hx + ky + lz )dhkl using fractional coordinates

According to Bragg’s law, the path difference between O and A is

δ = 2d sinθhkl = 2dhkl sinθhkl (hx + ky + lz )
 Using wave equations instead
We can describe a wave as

W0 = f·cos(2X/) or W0 = f·cos(t)
where W0 is the transverse displacement of a wave moving in the X direction,
the maximum amplitude is f at t=0 and X=0
For other waves with a maximum at t=tn and X=Xn, we can write

Wn = fn·cos(2X/ - n) where n = 2Xn/

Two arbitrary waves of same frequency can then be represented as

W1 = f1·cos(t - 1) = f1·[cos(t) cos(1) + sin(t) sin(1)]

W2 = f2·cos(t - 2) = f2·[cos(t) cos(2) + sin(t) sin(2)]

Sum: W = W1+W2 = cos(t)·( f1·cos(1)+ f2·cos(2))+sin(t)·( f1·sin(1)+ f2·sin(2))

 Wave equations continued

We know that we can write any wave as

W = F cos(t - ) = F [cos(t) cos() + sin(t) sin()]

Comparison with the equations on the last slide gives

F cos() = f1 cos(1) + f2 cos(2)

F sin() = f1 sin(1) + f2 sin(2)

F can be calculated as

F = [(f1 cos(1) + f2 cos(2))2 + (f1 sin(1) + f2 sin(2))2]1/2

 Argand diagrams

 Waves can be represented as vectors

in an Argand diagram
- represented with real and imaginary
components
- allows for straightforward wave
addition
- For any given wave, we can write
F = |F|·(cos(t) + i·sin(t)) = |F|·eit
(compare to slide 9 of handout 6!)

“Crystal Structure Analysis for Chemists and

Biologists”, Glusker, Lewis and Rossi, VCH, 1994.
 Wave addition using Argand diagrams
 Any number of waves can be added using an Argand
diagram
- For N waves, 𝐹 cos( 𝜑) = 𝑓 cos( 𝜑 ) ; 𝐹 sin( 𝜑) = 𝑓 sin( 𝜑 )

- Alternatively, we can write 𝐅= 𝑓𝐞 = |𝐹|𝐞

“Structure Determination
by X-ray Crystallography”,
Ladd and Palmer, Plenum,
1994.
 Phase difference
 From our treatment of path differences of waves scattered
by arbitrary atoms, we obtained
𝛿 = 𝜆(ℎ𝑥 + 𝑘𝑦 + 𝑙𝑧 )

 The corresponding phase difference can be written as

 This implies that our expression for F depends on the

diffraction direction as described by the Miller indices hkl
(or the diffraction angle, if you prefer)
 Structure factors
 F should be more properly written as F(hkl) or Fhkl to
express its dependence on the diffraction angle
 There will be a unique F(hkl) corresponding to each
reflection in a diffraction pattern
- note – and remember! – that all atoms in a crystal contribute to
every F(hkl)!

 F(hkl) is called the structure factor for the (hkl) reflection

 Can be broken down in its real and imaginary components
𝐅(ℎ𝑘𝑙) = 𝐴(ℎ𝑘𝑙) + 𝑖𝐵(ℎ𝑘𝑙)

where
𝐴(ℎ𝑘𝑙) = 𝑓 cos( 2𝜋(ℎ𝑥 + 𝑘𝑦 + 𝑙𝑧 )) 𝐵(ℎ𝑘𝑙) = 𝑓 sin( 2𝜋(ℎ𝑥 + 𝑘𝑦 + 𝑙𝑧 ))
 Atomic scattering factors
 The individual atomic components, fj, are called atomic
scattering factors
- depend on nature of atom, direction of scattering, and X-ray
wavelength

- provide a measure of how efficiently an atom scatters X-rays

compared to an electron

- usually written as fj, although they should be written as fj,,

- listed as a function of sin()/ for each atom in the International

Tables

- maximum value of fj is Zj, the number of electrons of the jth atom

 Intensity and structure factors
 We cannot measure structure factors, instead, we will
measure the intensity of diffracted beams

 The phase is given by

 Problem: We lose the phase information when

measuring intensities!
 Factors between I and F
 There are several factors between I and F that will change
the measured intensity:
- thermal vibration of the atoms: exp[-Bj(sin2()/2]

- Lorentz factor, for normal 4 circle diffractometers: 1/sin(2)

- absorption: e-t, where  is the linear absorption coefficient and t

the thickness of the specimen

- polarization: p = (1+cos2 (2))/2

- scale factor
 Thermal vibration
 Thermal vibration “smears out” the electron cloud
surrounding an atom
- we see time average over all configurations

- displacement of atoms leads to slight phase difference for atoms in

neighboring unit cells

- f = f0·exp[-Bj(sin2()/2]

- is the mean square

amplitude of displacement
 Systematic absences
 Some reflections will be systematically absent from your
diffraction pattern
 These absences are a result of
- lattice centering

- glide planes

- screw axes

 Note that simple rotations and mirror planes to not give

systematic absences!
 Space groups can be assigned based on systematic
absences
 Systematic absences (2)

“Structure Determination by X-ray Crystallography”,

Ladd and Palmer, Plenum, 1994.
Fourier transforms and crystals

“Crystal Structure Analysis for Chemists and

Biologists”, Glusker, Lewis and Rossi, VCH, 1994.
 The electron density
 The electron density in a crystal can be described as a periodic
function
- same contents in each unit cell
- represented by a sum of cosine and sine functions
- wavelength is related to lattice periodicity

 The construction of a periodic function by the summation of

sine and cosine waves is called a Fourier synthesis
 The decomposition of a periodic function into sine and cosine
waves is called a Fourier analysis
Fourier synthesis and analysis

“Crystal Structure Analysis for Chemists and

Biologists”, Glusker, Lewis and Rossi, VCH, 1994.
 Fourier series
 The complete set of components that are necessary to describe
a periodic function is called a Fourier series
 The intensity of a Bragg reflection is related to the amplitude of
an electron density wave in the crystal in hkl direction
- all Bragg peaks: Fourier series describing the electron density of a
crystal
- scattering of X-rays by atoms can be regarded as a Fourier analysis,
producing the Fhkl structure factor waves
 The electron density can be determined from the diffraction
pattern by a Fourier synthesis:
1
𝜌(𝑥𝑦𝑧) = 𝐹(ℎ𝑘𝑙) exp( − 2𝜋𝑖(ℎ𝑥 + 𝑘𝑦 + 𝑙𝑧) − 𝜑 )
𝑉
 Electron density waves
 In order to obtain the electron
density, we need to sum all
contributing electron density
waves (Fourier synthesis)
 Note that the electron density
waves do not have the same
frequencies (wavelengths)!
- periodicity depends on hkl
- wavelength is dhkl
“Crystal Structure Analysis for Chemists and
Biologists”, Glusker, Lewis and Rossi, VCH, 1994.
Summing electron density waves

“Crystal Structure Analysis for Chemists and

Biologists”, Glusker, Lewis and Rossi, VCH, 1994.
A 1D example of a Fourier synthesis
“Crystal Structure Analysis for Chemists and
Biologists”, Glusker, Lewis and Rossi, VCH, 1994.

(b) Effects of successive

addition of terms in (a).
Note how the inclusion of
more terms leads the the
formation of distinct
electron density peaks.
 Fourier transforms
 Generic definition:

FT

FT-1

 Convolution* of two Fourier transforms:

* A convolution is an integral which expresses the amount of overlap of one function g

as it is shifted over another function f. It therefore "blends" one function with another.
 The relationship between F and 
 We have shown that the structure factors can be described by a
Fourier synthesis from waves scattered by a crystal
– A diffraction pattern is the Fourier transform of an “object” (e.g., the
crystal for crystallographic experiments)
 We have also shown that the electron density can be obtained by
a Fourier synthesis of electron density waves (structure factors)
– The inverse Fourier transform of the diffraction pattern gives the original
object again

( )

( ) ( )
The FT relationship between f and atomic

“Crystal Structure Analysis for Chemists and

Biologists”, Glusker, Lewis and Rossi, VCH, 1994.
 Diffraction from holes – a FT perspective
 Diffraction from a single hole gives a ring pattern
 What happens when we have a second, identical hole at a distance
a from it?

For one hole, we can write: 𝐒⋅𝐫

𝐒⋅𝐫 𝐒⋅(𝐫 𝐚)
For two holes as described above:

𝐒⋅𝐚

The second hole superimposes a fringe function that will double the amplitude of
A0 when a·S is integral, and will lead to extinction halfway in between
 Fringe patterns

“Structure Determination by X-ray Crystallography”, Ladd and Palmer, Plenum, 1994.

 What’s a hole got to do with a crystal?
 The hole scatters the
light rays
 An electron scatters X-
rays
 Imagine a crystal as a
“hole pattern” of
electrons!
“Structure Determination by X-ray Crystallography”,
Ladd and Palmer, Plenum, 1994.
 The opposite approach…
 …transforming your diffraction pattern into an electron density map

“Structure Determination by X-ray Crystallography”,

Ladd and Palmer, Plenum, 1994.

The resolution of your electron density map will strongly

depend on how many reflections you use in creating it!
Fourier transforms of crystals

“Crystal Structure Analysis for Chemists and

Biologists”, Glusker, Lewis and Rossi, VCH, 1994.