2. Structure Factors (1)

In this section we will look at the structure factors of a small molecule structure.

The applet now shows two atoms (marked by the black crosses) in a unit cell, and the corresponding structure factors and electron density. The electron density shows peaks for the two atoms (each of 6 electrons). Thus the origin term has a magnitude of 12, being the total number of electrons in the unit cell. There is also a little noise due to the incomplete set of structure factors.

Select the (2,0) reflection. This reflection also has a magnitude of 12 electrons. Notice that the Bragg planes pass through the centres of both atoms. Find other reflections for which the Bragg planes pass exactly through all the atoms, and confirm that they have the same magnitude.

You may also have found some weaker reflections. For example, the (1,1) reflection only passes near the atomic centres, and so it is slightly weaker. The (2,1) reflection is further still from the atomic centres.

Finally select the (1,0) reflection. Adjust the phase of this reflection until the density peaks (Bragg planes) pass through one of the atoms. Where is the other atom with respect to the Bragg planes? Where does it lie on the cosine wave? Why does this reflection have zero magnitude?