X Ray Diffraction

Question 1

What is X-ray diffraction?

Answer 1

1. The definitive structural probe for solid state

2. Involves shining X rays onto crystalline materials and then observing the scattered radiation

Question 2

What does analysis of the scattered radiation in X ray diffraction show?

Answer 2

1. Where the atoms are (you can “see” them)
2. How they are connected to form molecules
3. How they pack to form crystals
4. To what extent they are vibrating

Question 3

What are the two different forms of molecular crystals?

Answer 3

1. Single crystal- 0.1 x 0.1 x 0.1 nm

2. Millions of crystals- size typically a few micro meters

Question 4

What is shown inside a 3D molecular crystal?

Answer 4

1. The unit cell
2. Atom positions
3. Different molecules 1 and 2

Question 5

What is long range order?

Answer 5

1. One dot to one molecule

2. Basic block that repeats itself like the full array of atoms

Question 6

What are the unit cell dimensions?

Answer 6

1. An origin
2. Three lengths (abc)
3. Three angles (alpha, beta, gamma)
   Lengths are in degrees

Question 7

What are the most common unit cell types?

Answer 7

1, Orthorhombic- alpha = beta = gamma = 90 degrees (most considered from now on) (cube)

2. Monoclinic- alpha = gamma = 90 degrees. Beta doesn’t = 90 degrees (3D rhombus)

Question 8

What are fractional co-ordinates?

Answer 8

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

Question 9

Describe symmetry in relation to a unit cell?

Answer 9

1. A typical unit cell contains more than one molecule
2. These molecules are not independent, but are related by symmetry elements
3. Do not need to know the position of every molecule in the unit cell
4. Just need find ONE molecule, as long as we know the symmetry relationships between the molecules.

Question 10

Describe the centre of symmetry?

Answer 10

When the molecule flips from one side to the other:

A
A (other way round)

Question 11

Describe the mirror plane?

Answer 11

A complete normal mirror image, two enantiomers

Question 12

In terms of symmetry, how do we de

Answer 12

s

Question 13

What is the space group?

Answer 13

Describes symmetry relationships in a crystal

Question 14

What ways is it possible to see inside crystals?

Answer 14

X rays- highly penetrating but interact with matter- bet thought of as waves

Question 15

How do X rays and matter work?

Answer 15

1. X rays scatter off of electrons
2. Atoms with lots of electrons scatter strongly (example: Au) and can be seen easily
3. Atoms with fewer electrons scatter little (example: H) and so are much more difficult to see

Question 16

How do you explain diffraction?

Answer 16

1. The most easily visualised as reflections from a plane in a unit cell
2. The planes are drawn within a unit cell but are imaginary

Question 17

What is Bragg’s law?

Answer 17

1. 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

Question 18

Judging from Bragg’s law, what important link can be established?

Answer 18

• 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

Question 19

What are miller indices?

Answer 19

1. h, k, l

2. Labels for particular planes in the unit cell

Question 20

What does the strength of a scattered x ray represent?

Answer 20

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

Question 21

What are the two different methods and applications for single crystal diffraction?

Answer 21

Diffractometer and Data

Question 22

What are the characteristics and main applications for single crystal?

Answer 22

Characteristics:

1. Single crystal
2. Typically 0.1 x 0.1 x 0.1 mm
3. Data collection is typically a few hours (8 hours)
4. Thousands of accurate reflection intensities
5. Analysis time typically minutes

Main applications:
1. Full crystal structure determination- accurate atom positions and therefore accurate molecular geometry

BEST METHOD TO GROW CRYSTAL

Question 23

How do we apply the use of single crystal?

Answer 23

Chirality

1. 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
2. We need drugs to be formulated as only one enantiomer

Question 24

How do we identify a polymorph using PXRD?

Answer 24

1. A polymorph is a particular crystalline form of a compound and the PXRD pattern is a “Fingerprint”
2. The different peak positions change because the unit cells are different
3. Peak intensities are different because of the atomic positions

Question 25

What is phase transformation in relation to a polymorph?

Answer 25

1. Polymorphs frequently interconvert over time to a more stable form.
   example: via temperature
2. Due to changes in patterns and crystal structure changing

Question 26

What does the PXRD application show for an Amorphous?

Answer 26

1. Only short range order
2. No clear Bragg diffraction
3. Only so called “amorphous hump” is seen