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Molecular Structure Laboratory

Introduction to Crystallography


Molecular Structure Laboratory / Introduction to Crystallography Updated: October 26, 2015


Introduction
Single crystal X-ray analysis  is an ultimate non-destructive  analytical technique that provides a wealth of information about the crystalline lattice, unit cell dimensions,  atomic positions inside the unit cell from a very small amount of material.  By analyzing a sample with a volume of 0.1 mm3  one can establish the crystal composition, identify all molecular or ionic species present, their symmetry, conformations, and mutual arrangement in the lattice.  More importantly, oxidation states, interatomic distances and angles as well as torsion angles are established with high precision.  Visual representation of the X-ray single crystal analysis results is found in the form of molecular drawing everywhere - from popular TV programs to scientific journals.


Instruments
This lab is equipped with two new state-of-the-art single-crystal diffractometers.  The instruments are equipped with leaded glass and are very safe to use.  The top one, creatively named "Bucky", is optimized for analyzing crystals of organic compounds. 
There are three basic components in a diffractometer - a radiation source, sample holder, and detector supported by a large platform.  (1) The X-ray source is a cathode ray tube that produces radiation with a characteristic wavelengths of its target material.  Here we have a Cu-radiation X-ray source with the wavelength of 1.54 Å. The size of the X-ray beam is 0.5 mm (0.02 inches).  (2) The sample is mounted on a goniometer head and is centered in the X-ray beam by means of a video camera.  (3) A state-of-the-art two-dimensional CCD detector (not unlike two-dimensional chips in your digital cameras) is optimized for detection of X-ray photons - it coverts X-rays into an electrical signal recorded by a computer. 
The instrument was put in operation in 2007.  It retails for ~$280 K.

The other instrument, named Gromit, is ideal for analyzing organometallic and inorganic materials.  It also contains a goniometer that supports a CCD detector, crystal,  and a radiation source.  The tube radiation source is unique, and this is only the second instrument of this type in the USA.  The source produces a very brilliant beam of Mo radiation with the wavelength of 0.71073 Å, which is harder than the Cu radiation and it the radiation of choice for materials with high absorption, such as inorganic and organometallic compounds.  The beam size is 120 microns, which requires a very precise alignment of the crystal and the instrument.  This instrument costs almost $400K. 

X-ray diffractometers have been known to last as long as 20 years, but due to technological advances become outdated in 6-8 years.
Crystals
It is always a pleasure to look at crystals - they signify a transition from chaos to perfection.  There are several requirements for a crystal to be suitable for an X-ray diffraction experiment.  Ideally, it should measure up to 0.5 mm along each side and have as few internal imperfections as possible.  The crystal does not have to be beautiful or have well formed facets and edges as long it looks wholesome, with no cracks, striations, and bubbles.  We use an optical microscope equipped with a polarizer to select crystals.
The crystals are selected under paratone oil.  There are several reasons for that:  the oil protects the crystals from air and moisture, which is important when crystals are air- and moisture-sensitive;  when crystals are cut they don't fly off the slide but remain in the field of view;  when the crystals are put on the diffractometer in the stream of cold nitrogen, the oil solidifies and keeps the crystal protected and firmly attached to the mount.  And if after the experiment you decide to do additional analyses on the crystal the oil will thaw and the crystal becomes available - that's impossible to do with glue.
The crystal is mounted onto a nylon loop and transferred to an instrument.
Data acquisition
The crystal is cooled with a cold stream of nitrogen.  We routinely collect the data at 100 K.  Low temperatures freeze out atomic thermal motion and cooled crystal diffract much better.
Crystalline substances act as three-dimensional diffraction gratings for X-ray wavelengths comparable to the interactomic distances.  X-ray diffraction is based on constructive interference of monochromated X-rays with a crystal.  The constructive interference is observed when interaction between the incident beam and the crystal satisfies Bragg's law (nλ = 2dsinθ).
Typical structures contain many thousands of unique reflections, whose spatial arrangement is referred to as a diffraction pattern. The diffraction pattern is seen on the computer screen in real time.  Three hkl indices are assigned to each reflection, indicating its position within the diffraction pattern. The spot positions provide information about the dimensions of the unit cell, the smallest building block of the crystal, whereas the spot intensities contain information about the unit cell content.   The diffraction pattern has a reciprocal Fourier transform relationship to the crystalline lattice and the unit cell in real space. Diffraction patterns are unique with few exceptions and the unit cell dimensions can serve as a compound identifier.  The X-ray photons are diffracted by electrons, thus crystals with heavier elements diffract better than crystals of organic compounds, and larger crystals diffract better than small ones. 
Data analysis
A typical data acquisition for a publishable quality dataset takes anywhere between 4 hours to 4 days, depending on the crystal quality and composition.  The data are processed with specialized programs and then the structure has to be solved and refined by least-squares techniques, which takes between an hour and several days, depending on the structure. In 80% cases, our customers are given the results within 48 hours.  The result is a highly precise crystal structure that can be visualized with numerous software programs, and a detailed report describing the structure.  Our results can be included in scientific publications with minimum modifications.
Encore
The advantages of X-ray analysis are multiple: it's non-destructive, requires no separate standard, and produces a detailed crystal structure.
The limitations include the necessity to have a single and stable crystal measuring between 50-500 microns in size.  Data collection typically takes between several hours and several days.
We analyze about a structure per day.  We have over 30 collaborators, a quarter of which is outside of Madison, in places such as La Crosse, Iowa, Tennessee, Mexico, Russia, and South Africa. 
The single-crystal X-ray analysis yields publishable quality data of the molecular structure in question.  We establish interatomic bond distances and angles, torsion angles, overall molecular composition and conformation, and intermolecular interactions in the lattice.  The information is used by organic and inorganic chemists to identify and characterize compounds, confirm or determine the absolute configuration at the chiral centers, or to establish structure-property relationship and determine crystal-chemical controls on the chemistry.
   

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