Day 7/8 part 2
๐ First: normal X-ray scattering (no anomalous effect)
When X-rays hit atoms in a crystal:
- Electrons oscillate
- They re-emit X-rays โ scattering
This scattering creates the diffraction pattern.
Normally we assume:
Scattering is purely elastic โ no energy is absorbed.
Mathematically:
F_ = F_{-h-k-l}
This means:
- Friedel pairs have identical intensity
So:
๐ No extra information about phase can be obtained.
โก What is anomalous scattering (intuitive idea)
Anomalous scattering happens when:
The atom absorbs some of the X-ray energy and then re-emits it with a small phase shift.
So scattering is no longer perfectly elastic.
This only happens strongly for heavy atoms and only at specific X-ray energies.
๐ง Think of it like this
Normal atom:
- behaves like a simple mirror โ reflects light cleanly
Anomalous atom:
- behaves like a mirror + sponge
- it absorbs some energy
- re-emits with delay and changed amplitude
This โdelayโ = phase change
That tiny change is what crystallographers exploit.
๐ Mathematical view (simplified)
Normal scattering factor:
f
With anomalous scattering:
f = f_0 + f' + if''
Where:
- ( f_0 ) โ normal scattering
- ( f' ) โ real correction (dispersion)
- ( f'' ) โ imaginary correction (absorption-related)
These extra terms:
๐ change reflection intensities ๐ break Friedelโs law.
๐ฏ Why is this useful?
Because now:
I(hkl) eq I(-h-k-l)
This intensity difference allows us to:
- locate heavy atoms
- estimate phases
- solve structure.
This is the basis of SAD/MAD phasing.
๐ฅ What is the absorption edge?
Now the REALLY key idea.
Atoms have core electrons:
- K-shell
- L-shell
- etc.
Each shell has a specific binding energy.
Absorption edge = threshold energy
If X-ray energy becomes high enough to:
eject a core electron
Then absorption suddenly increases.
This sharp increase in absorption vs energy is called:
Absorption edge
It looks like a step in an absorption spectrum.
Why is anomalous scattering strongest there?
At the absorption edge:
- Atom strongly interacts with X-rays
- Electron excitation becomes very efficient
- ( f' ) and ( f'' ) change rapidly
This produces:
- maximum anomalous signal
- biggest intensity differences.
So crystallographers:
๐ tune synchrotron wavelength exactly to that edge.
๐ก Example (from your lecture)
They used tungsten.
Procedure:
- Measure absorption spectrum
- Find edge position
- Collect diffraction data at:
- Peak wavelength
- Inflection wavelength
- Remote wavelength
This is MAD phasing.
๐ง Super important intuition
Normal diffraction:
- all atoms scatter similarly
- symmetry preserved
- no phase info.
Anomalous diffraction:
- heavy atoms scatter โweirdlyโ
- symmetry slightly broken
- tiny intensity differences appear
- these differences encode phase information.
โญ VERY short exam definition
Anomalous scattering: Deviation from normal elastic X-ray scattering that occurs near an atomโs absorption edge, causing changes in scattering amplitude and phase, which lead to intensity differences between Friedel pairs and allow phase determination.
Absorption edge: The X-ray energy at which core electrons of an atom can be excited or ejected, causing a sharp increase in absorption and strong anomalous scattering effects.