Biophysical diffraction Flashcards
What is the ‘phase problem’ in X-ray diffraction?
X-rays can not be focused by lenses and the phase relationship between scattered waves is lost.
Over 90% of X-rays don’t interact with the sample and just pass through it. Single molecules scatter x-rays very weakly and hydrogen for example is barely seen at all.
Hence why it is useful to use crystals.
What is a method that can be used to overcome the phase problem in X-ray diffraction?
Powder diffraction uses 1000’s of crystallites
Why is crystals preferred over single molecules in X-ray diffraction?
X-rays are scattered very weakly in single molecules. The structure of these molecules get damaged when they are blasted by an Xray. In a crystal structure there is far less damage which increases the signal strength. The blow is lessened as there is far more crystals.
What are three processes by which X-rays interact with atoms?
Thompson scattering, Compton scattering and Photoelectron absorption
Briefly describe Thomspson scattering?
Elastic scattering where there is no loss of energy. The incoming magnetic field excites electrons in an atom and making them oscillate at the same frequency.
This is coherent scattering.
Can be seen due to their small mass.
Only 8% of absorbed X-rays are scattered by this means
Briefly describe Compton scattering?
Inelastic scattering and so there is a loss of energy. Photon ejects an OUTER shell electron and scatters rays of different frequencies unlike the Thompson scattering. This also accounts for 8% of absorbed X-ray scattering.
This can be described as incoherent scattering
Briefly describe Photoelectron absorption?
Inelastic scattering - loss of energy. Photon ejected from INNER shell. All the energy is absorbed so no scattered x-rays like the other two. This is the main source of radiation damage (e-) and 84% of X-rays are absorbed.
What is the atomic scattering factor?
In the forward direction all electrons in an atom will scatter X-rays exactly in phase. At other angles partial destructive interference occurs where intensity falls off with Braggs angle
What is a physical explanation for the atomic scattering factor?
Temperature factors
What is temperature factors?
Atoms vibrate depending on molecular motion and temperature, which then spreads out the atomic electron density and means that the scattering factor falls off faster as Braggs angle increases
How does the scattering factor vary with Bragg’s angle?
Intensity falls with Bragg’s angle
Why are X-rays commonly used?
To produce an image the wavelength flight must be comparable or shorter than the object. X-rays are on the left hand side of the electromagnetic spectrum and so has a big wavelength/ low energy.
Describe the generation of X-rays? 3 key parts
An X-ray tube with a source of electrons, a metal anode/target and a vacuum. e- is accelerated by high voltage to target and most of the kinetic energy is lost as heat.
Can’t hit the same part of the anode every time as it would get damaged.
How can you relate the words space group, unit cell and assymetric unit together? What does each mean in turn?
The space group is a group of symmetry operations which operate on the asymmetric unit to generate a complete unit cell.
Unit cell: Can be described by symmetry. A crystal is made up of lots of unit cells which may contain more than one molecule.
Assymetric unit: A smaller volume of the unit cell.
What are threee properties of interest in diffraction patterns?
Geometry - regular pattern
Symmetry - the pattern can be symmetrical/reflecting
Intensities - these can be very intense or even too weak
