1. Organic Chemistry
Lesson 21
X-ray crystallography

2. The Basics
X-ray crystallography is a method for determining the arrangement of atoms within a crystal structure.
Substances including inorganic salts and minerals, semiconductors, and organic and biological compounds can form crystals under suitable and specific conditions.
This method of structure determination has provided the most reliable evidence scientists have about the way molecules are shaped and what their bonds angles and lengths are.

3. The Process
Workflow for Solving a Molecular Structure Using X-ray Crystallography
The steps to the process of determining the three dimensional structure of a molecule are outlined in this figure.

4. Diffraction
When bombarded with x-ray radiation, crystals exhibit a characteristic diffraction pattern.
To obtain x-ray diffraction measurements, three components are necessary:
a crystal sample
a source of x-ray beams
a detector
The best x-ray crystallographic structures are derived from the purest crystal samples, meaning samples that contain only molecules of one type and as few impurities as possible.

5. Diffraction Pattern Diffraction pattern for a protein
An X-ray diffraction pattern of a crystallized protein molecule. The two dimensional reflection pattern can be used to determine the atomic structure of the protein.
This process reveals the geometry of the atoms within the molecules.
The x-ray beams are diffracted in a characteristic pattern that gives rise to reflections, dark spots on the detector which represent places where constructive interference of the diffracted light has occurred.
The detector records the reflections on a two-dimensional surface.
The crystal is typically rotated with respect to different axes and shot again with X-rays, so that diffraction patterns from all angles of the X-rays hitting the crystal are recorded.
Diffraction pattern for a protein

6. Bond lengths and bond angles
Electron density map and structure of anthracene
Then mathematical algorithms are applied in order to decode the information contained within the recorded reflections. A map is constructed to describe the electron density of the molecules in the crystal
From this map of electron density bond angles and bond lengths can be measured.
Atomic models of the molecules are also created; these can explain the experimentally observed electron density.