Teaching set #4 - Molecular form factor
The molecular form factor (that is, the Fourier transform of a molecule's scattering centres) has a major impact on diffraction patterns, since their intensity distribution is defined by the unit cell content as we have seen in the teaching set #3, and this content consists of atoms that can be found assembled in molecules.
In this teaching set we observe how different arrangement of atoms produce different diffraction patterns, where the very distribution of intensities originates from the molecular form factor. X-ray scattering factors were used for each pattern calculation.
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01. Single carbon atom and its diffraction pattern.
02. Pair of carbon atoms (ortho position in a benzene ring) and their diffraction pattern.
03. Pair of carbon atoms (meta position in a benzene ring) and their diffraction pattern.
04. Pair of carbon atoms (para position in a benzene ring) and their diffraction pattern.
05. Three neighbouring carbon atoms of a benzene ring and their diffraction pattern.
06. Four neighbouring carbon atoms of a benzene ring and their diffraction pattern.
07. Five neighbouring carbon atoms of a benzene ring and their diffraction pattern.
08. Carbon atoms of a benzene molecule and their diffraction pattern.
09. Carbon atoms of a naphtalene molecule and their diffraction pattern.
10. Carbon atoms of an anthracene molecule and their diffraction pattern.
11. Carbon atoms of a phenalene molecule and their diffraction pattern.
12. Carbon atoms of a coronene molecule and their diffraction pattern.
13. Carbon atoms of a circumcoronene molecule and their diffraction pattern.
14. A 18-Crown-6 ether molecule and its diffraction pattern.
15. A caffeine molecule and its diffraction pattern.
16. A short strand of DNA and its diffraction pattern.
P.S.: something very similar has been worthy of nothing less than a Nobel prize! If that sounds new, write in a search engine "photo 51" and read what comes out to learn more.
17. Effects of atomic substituents with different atomic numbers on the diffraction pattern of a test molecule. From left to right, an hydrogen is replaced by fluorine, chlorine, bromine and iodine.
From above, the first series of patterns are shown using an arbitrary intensity scale, while the second series uses a constant scale and a divergent colour scheme to highlight how heavier atoms yield stronger and differently distributed intensities. Lastly, diffraction from crystals of each of the five molecules are considered for showing the effect of the atomic replacement on the diffraction of crystalline samples.
