X Ray Diffraction Flashcards
What is X-ray diffraction?
- The definitive structural probe for solid state
2. Involves shining X rays onto crystalline materials and then observing the scattered radiation
What does analysis of the scattered radiation in X ray diffraction show?
- Where the atoms are (you can “see” them)
- How they are connected to form molecules
- How they pack to form crystals
- To what extent they are vibrating
What are the two different forms of molecular crystals?
- Single crystal- 0.1 x 0.1 x 0.1 nm
2. Millions of crystals- size typically a few micro meters
What is shown inside a 3D molecular crystal?
- The unit cell
- Atom positions
- Different molecules 1 and 2
What is long range order?
- One dot to one molecule
2. Basic block that repeats itself like the full array of atoms
What are the unit cell dimensions?
- An origin
- Three lengths (abc)
- Three angles (alpha, beta, gamma)
Lengths are in degrees
What are the most common unit cell types?
1, Orthorhombic- alpha = beta = gamma = 90 degrees (most considered from now on) (cube)
- Monoclinic- alpha = gamma = 90 degrees. Beta doesn’t = 90 degrees (3D rhombus)
What are fractional co-ordinates?
When co-ordinates are given in the form of example: (0.33, 0.5, 0.9) and are given in a fractions of a cell edge
Describe symmetry in relation to a unit cell?
- A typical unit cell contains more than one molecule
- These molecules are not independent, but are related by symmetry elements
- Do not need to know the position of every molecule in the unit cell
- Just need find ONE molecule, as long as we know the symmetry relationships between the molecules.
Describe the centre of symmetry?
When the molecule flips from one side to the other:
A
A (other way round)
Describe the mirror plane?
A complete normal mirror image, two enantiomers
In terms of symmetry, how do we de
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What is the space group?
Describes symmetry relationships in a crystal
What ways is it possible to see inside crystals?
X rays- highly penetrating but interact with matter- bet thought of as waves
How do X rays and matter work?
- X rays scatter off of electrons
- Atoms with lots of electrons scatter strongly (example: Au) and can be seen easily
- Atoms with fewer electrons scatter little (example: H) and so are much more difficult to see
How do you explain diffraction?
- The most easily visualised as reflections from a plane in a unit cell
- The planes are drawn within a unit cell but are imaginary
What is Bragg’s law?
- When a reflection is only seen when Bragg’s law is satisfied i.e. when Gamma = 2d sin (0)
- Gamma is the wavelength of the radiation
- d is the interplanar spacing
- 0 is half the observed diffraction angle
Judging from Bragg’s law, what important link can be established?
- By measuring lots of x ray reflections, you can work out lots of d spacings
- One can then mathematically work out the size and the shape of the unit cell
What are miller indices?
- h, k, l
2. Labels for particular planes in the unit cell
What does the strength of a scattered x ray represent?
Reflects the distribution of atoms in the cell and their types
Example: if a plane has lots of atoms with lots of electrons, it is likely to scatter strongly
What are the two different methods and applications for single crystal diffraction?
Diffractometer and Data
What are the characteristics and main applications for single crystal?
Characteristics:
- Single crystal
- Typically 0.1 x 0.1 x 0.1 mm
- Data collection is typically a few hours (8 hours)
- Thousands of accurate reflection intensities
- Analysis time typically minutes
Main applications:
1. Full crystal structure determination- accurate atom positions and therefore accurate molecular geometry
BEST METHOD TO GROW CRYSTAL
How do we apply the use of single crystal?
Chirality
- Many drugs exist as racemates- mixture of left and right handed enantiomers
- for example: if we crystallise a drug and find that it crystallises in a space group with a centre of symmetry or a mirror plane then its racemate - We need drugs to be formulated as only one enantiomer
How do we identify a polymorph using PXRD?
- A polymorph is a particular crystalline form of a compound and the PXRD pattern is a “Fingerprint”
- The different peak positions change because the unit cells are different
- Peak intensities are different because of the atomic positions
