Analysing crystals

Why is it difficult to locate h-bonds, and light atoms in the presence of heavy atoms when using X-ray diffraction

X-rays are diffracted by electrons, and so atoms with lots of electrons show up better than those with very few

How can we view these atoms with few electrons

We can instead observe the neutrons, these will be diffracted by crystalline solids giving their structural information.

They interact with nuclei rather than electrons so will see the atoms differently

This means that H bonds and light will show up clearly

What are the three factors we use to express structure data

Once solved and refined a crystal structure is expressed in terms of:  

• cell parameters (a, b, c; α, β, γ)  

• space group (every crystal belongs to one of 230 symmetry descriptions)  

• atomic coordinates 

In order to visualize a structure or calculate the distances between atoms all there must be taken into account. 

What unit do we use for volume

Angstrom

How are the positions of atoms expressed in crystallography, and why this way.

Expressed as fractional co-ordinates as they represent positions as fractions of the unit cells lattice vectors, creating standardised measurements not dependant by specific units of length

During analysis what system must we use for atomic position

Cartesian co-ordinate’s

What is the formula for converting fractional to cartesian coordinates in orthogonal crystal systems

(orthogonal is cubic, tetragonal, and orthorhombic)

X_cart = a * x_frac

y_cart = b * y_frac

z_cart = c * z_frac

What’s the formula for calculating distances using cartesian coords