3' Sample preparations

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3. Sample preparations
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Crystals and Their Properties

• Crystallization is a form of purification. A
  material goes from a disordered state in the form
  of a solution, melt or vapor phase to an ordered,
  solid state material.
• Nucleation site is a point in liquid or the
  vapor/substrate boundary that initiates the
  growth of crystalline material. There is an
  equilibrium between the various disordered states
  and the desired crystalline state. It is the role
  of the chemist to push the equilibrium in his/her
  favor.
• It is important to attempt to grow crystals with
  a minimum of defects. A number of things fall
  into this category. Solvents and even similar
  shaped side products can occupy sites in the unit
  cell along with the desired material. Twinning is
  also considered a type of defect.
• Faces are an indication that crystals are ordered
  externally.

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Common Solvents for Growing Crystals

• Non-polar solvents-benzene, toluene, pentane,
  hexane(s), heptane, diethylether, ethyl acetate,
  etc.
• Polar solvents-Dichloromethane, chloroform,
  water, methanol, ethanol, isopropanol, etc.
• Low-temperature combinations-diethyl ether and
  dichloromethane solutions are infinitely soluble
  in each other and in combination have a lower
  freezing point than pure solvents. This is
  particularly useful when working with materials
  that decompose when warmed to room temperature.
• Inorganic solvents-mineral acids, superacids,
  salts (at elevated temperatures), bases, etc.

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Strategies for Growing Crystals

• It is assumed that the chemist has acquired the
  proper MSDS sheets and has proper training and
  equipment to deal with solvent fumes and other
  potential problems.
• Evaporation - This is the simplest method. A
  impure or amorphous material is dissolved in a
  solvent. As solvent evaporates from the solution
  at a constant temperature crystals form at the
  air/liquid interface or in the bottom of the
  vessel. The super saturation forces the desired
  material out of solution while keeping impurities
  in solution.
• Diffusion - This is similar to the previous
  method, but a second solvent is added to a closed
  system. The vapor phases of both solvents mix
  slowly. If the material is less soluble in the
  admixture, then crystals can form.

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• Slow Cooling Method - Solutions can be slowly
  cooled to as low as the solvents will allow
  (toluene and diethyl ether/ dichloromethane
  solutions can go lower than dry ice
  temperatures). This method often produces
  crystals with co-crystallized solvent.
• Growth from the Melt - Sometimes crystals can be
  produced by melting and with proper cooling (and
  perhaps seeding) will produce useful crystals.
• Sublimation Method - If the material has a
  moderate vapor pressure at a temperature low
  enough to prevent decomposition, then sublimation
  may be a good methods to try.
• Reaction Method - Quite often crystals will form
  directly in the course of a reaction. Cooling
  and/or addition of crashing solvents helps
  encourage this to occur.

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• Elixir method - Many chemists work in an area of
  synthetic chemistry that provides crystalline
  material from mixed-solvent systems. Generally,
  the crude product is formed in the elixir and
  cooled for a period which produces crystalline
  material.
• NMR Tube Method - The clean NMR tubes and clean
  solvents provide a surface with few nucleation
  sites. The combination of evaporation of solvent
  and cooling usually provides high-quality
  specimens.
• Layered Solvent Method - The crude is dissolved
  in a denser solvent than the second one that is
  layered at its top. Diffusion at the interface
  produces active nucleation sites which provide
  few but high-quality specimens.
• Hanging Drop Method - One drop on a glass slide
  in a closed environment. Provides a few crystals
  per drop.

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Hanging drop method
A schematic drawing of the hanging drop method
for protein crystallization
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Selecting a Good Specimen for Diffraction

• The goal is to find the best specimen for your
  diffraction experiment.
• Observe the sample under the microscope. Is all
  of the solid crystalline? Is part of it
  amorphous? Do you see more than one type of
  crystal habit or color?
• It is good to coat specimens in oil while
  evaluating them. The refractive index of oil
  seems to highlight defects within or on the
  surface of the crystal. It helps as a lubricant
  to remove flakes of debris or small crystallites.
  It will be the glue, so to speak, that holds the
  specimen to the glass capillary or fiber when
  frozen at low temperature.
• The polarizing microscope is best for finding
  flaws.

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X-Ray Absorption Strategies

• Specimens with needle or plate shapes can cause
  difficulty when it comes time for the absorption
  correction to be made if the material is expected
  to have a large µ, linear absorption coefficient.
  Polished spheres have negligible absorption
  problems.

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Understanding Absorption Coefficients

• The equation for calculating the absorption of
  X-rays on a sample of known content and dimension
  is I I0e-µt.
• The correction of absorption on the SMART is done
  in one of two ways.
• First, if one can accurately measure the
  dimensions of the specimen and identify the face
  indices, then an analytical absorption correction
  can be applied. This is only recommended if the
  following method gives poorer the expected
  results.
• The method of Blessing, which is used in SADABS,
  gives remarkable results for area detector data
  when there is ample redundancy in the data and a
  variation in the diffractometer angles used.

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Calculation of a Linear Absorption Coefficient