Download Lesson 21 - MsReenChemistry

Organic
Chemistry
Lesson 21
X-ray crystallography
The Basics
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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.
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.
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.
Diffraction Pattern
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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.
Bond lengths
and bond angles
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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.