Topic 1: Local coordination in ionic, covalent and hydrogen bonded structures

Required videos: Topic 1

Download and install Vesta. Vesta is a free crystal structure viewing software. Download these structure files: NaCl, diamond-C, graphite, heroin, sapphire, iron, GaAs

i) Load diamond into Vesta. We'll take a look at the features of Vesta and then set you loose.

Hot keys:

Select - "s" & click individual atoms. To select multiple atoms, shift click or drag a box w/ the mouse.
Rotate - "r", then click and drag
Atom-Atom distance: "d", then click on the two atoms
Angle: "a", then click on the three atoms
Properties menu: "Apple-Shift-p"
Boundary menu: "Apple-Shift-b"
Bonds menu: "Apple-b"
Structure menu: "Apple-E"

ii) Load two of the structures into Vesta based on the following pairing:

Pairs of compounds: A - NaCl & sapphire, B - diamond-C & graphite, C - heroin & GaAs, D - iron & NaCl

iii) Identify which atom corresponds to which color. You can select atoms using the Select tool (hot key 's'), the results of selections are displayed at the bottom of the screen.

iv) Adjust the boundary (lower left button) to 2 unit cells in each direction.

v) Without considering the structure, what sort of bonding do you expect in each of these materials?

vi) Let's add bonds to help visualize the structure. Apple-b opens the bond menu, as does Edit-Bonds. A key value is the maximum distance to search for bonds. How far do you think we should search?

vii) In retrospect, are the bonds you've added realistic or misleading?

viii) Consider the local coordination of each atom. Can you correlate the electronegativity contrast with the local coordination number? Why or why not?