7/30/2019 single crystal XRD1.doc
1/5
Determination of the exact three-dimensional arrangement of building blocks (atoms, ions,
molecules) in a crystalline chemical compound using X-ray radiation.
One of the most common and most precise method for the determination of the three-
dimensional structure of crystalline compounds.
Information from a single crystal structure determination:-
Crystal system, Bravais-type, space group, metrics, lattice parameters
Crystallographic density and chemical composition
Symmetry of molecules
Constitution and absolute configuration of a chemical compound
Three-dimensional structure and packing of building blocks
Precise and sometimes accurate bond lengths
Conformation of molecules (torsion angles)
Intermolecular bonding parameters
Van der Waals radii
Volume of molecules
Electron distribution
Dynamic in crystalline solids
Static and dynamic disordering in crystalline solids
Single crystal structure analysis versus powder diffraction:-
Single Crystal Structure Analysis Powder Diffraction
One small single crystal (0.05 -0.8 mm) Several crystals
Information about one crystal Information about several crystals
Detailed and very precise information Limited information
Determination of the crystal structure Identification of compounds or
7/30/2019 single crystal XRD1.doc
2/5
with high precision and accuracy mixtures of different compounds
Information on ordering in crystals Investigations on homogeneity
Information on thermal motion and Information on stress, strain and
dynamics in crystals crystal size
Very precise bonding parameters Quantitative phase analysis
Determination of the crystal structure
(Usual not as precise as from single
crystal structure analysis
Techniques of crystallization
Slow Evaporation:- Prepare a solution of the compound in a suitable solvent. The
solution should be saturated or nearly saturated. Transfer the solution to a CLEAN
crystal growing dish and cover. Aluminium foil with some holes poked in it works
well, or a flat piece of glass with microscope slides used as a spacer also will do the
trick. Place the container in a quiet out of the way place and let it evaporate. This
method works best where there is enough material to saturate at least a few milliliters
of solvent.
Slow Cooling:- This is good for solute-solvent systems which are less than moderately
soluble and the solvent's boiling point is less than 100 deg C. Prepare a saturated
solution of the compound where is the solvent is heated to just it's boiling point or a
just below it. Transfer the solution to a CLEAN large test tube and stopper. Transfer
the test tube to a Dewar flask in which hot water (heated to a temperature of a coupleof degrees below the solvent boiling point). The water level should exceed the solvent
7/30/2019 single crystal XRD1.doc
3/5
level in the test tube, but should not exceed the height of the test tube. Stopper the
Dewar flask with a cork stopper and let the vessel sit for a week. A more elaborate
version of this involves a thermostated oven rather than a Dewar flask.
Vapor Diffusion:- This method is good for milligram amounts of material. A solution
of the substance is prepared using solvent S1 and placed in test tube T. A secondsolvent, S2, is placed in a closed beaker, B. S2 is chosen such that when mixed with
S1 the solute will become less soluble. The test tube containing S1 is then placed in
the beaker and the beaker is sealed. Slow diffusion of S2 into T and S1 out of T willcause crystals to form. If S2 is more volatile than S1 the solvent level will increase and
prevent microcrystalline crusts from forming on the sides of T.
Solvent Diffusion (Layering Technique):- This method also is good for milligram
amounts of materials which are sensitive to ambient laboratory conditions (air,
moisture). Dissolve the solute in S1 and place in a test tube. Slowly dribble S2 into the
tube so that S1 and S2 form discreet layers. This will only be successful if 1) The
density of S2 < S1 and 2) Care is exercised in creating the solvent layer. I have found
that a syringe is the best way to add the second solvent. The narrower the tube , the
easier it is to build up the layer. Five millimeter NMR tubes are excellent vessels to
use for this crystal growing technique. CH2Cl2/Et2O is a good solvent combination to
try this method (if your compound is insoluble in ether).
Sublimation:- Andrea Sella ([email protected]) suggests a couple of ways to grow
crystals of somewhat volatile air sensitive crystals. The first way is to simply seal asample under vacuum into a glass tube and placing the tube into an oven for a few
days or weeks. Larger crystals tend to grow at the expense of smaller ones. If it doesn't
work raise the temperature of the oven or move to another hotter one. In some cases atube furnace can be used. Andrea uses an all glass furnace which was originally
designed by Prof. Geoff Cloke of Sussex University (email him for the details if you
want to try this method). The tube can be placed close to one end of the furnace so that
there is a mild temperature gradient.
The second method is to seal off a long piece of glass tubing at one end and put a joint
with a vacuum adapter (or a Young's/Ace/Kontes valve) at the other. The sample is
placed at the sealed end of the tube and is followed by a glass wool plug which cleans
the tube as it is pushed along and serves to prevent bulk/crude material blowing alongthe tube itself. The tube is then evacuated and inserted into a length of copper pipe
which will serve to produce a temperature gradient. The sealed end of the tube (wherethe sample is) and the copper jacket are then heated in an oil bath (vertical set-up) or in
a tube furnace (either horizontal or vertical). The tube can be left under either dynamic
or static vacuum (it's worth trying both). Andrea learned this method from his Ph.D.
supervisor M. L. H. Green of Oxford.
Fundamental Principles of Single-crystal X-ray Diffraction:-
7/30/2019 single crystal XRD1.doc
4/5
X-ray diffraction is based on constructive interference of monochromatic X-rays and
a crystalline sample. These X-rays are generated by a cathode ray tube, filtered to produce
monochromatic radiation, collimated to concentrate, and directed toward the sample. The
interaction of the incident rays with the sample produces constructive interference (and a
diffracted ray) when conditions satisfy Bragg's Law (n=2d sin). This law relates the
wavelength of electromagnetic radiation to the diffraction angle and the lattice spacing in acrystalline sample. These diffracted X-rays are then detected, processed and counted. By
changing the geometry of the incident rays, the orientation of the centered crystal and the
detector, all possible diffraction directions of the lattice should be attained.
Single-crystal X-ray Diffraction Instrumentation:-
X-ray diffractometers consist of three basic elements, an X-ray tube, a sample holder,and an X-ray detector. X-rays are generated in a cathode ray tube by heating a filament to
produce electrons, accelerating the electrons toward a target by applying a voltage, andimpact of the electrons with the target material. When electrons have sufficient energy to
dislodge inner shell electrons of the target material, characteristic X-ray spectra are produced.
These spectra consist of several components, the most common being K and K. K consists,
in part, of K1 and K2. K1 has a slightly shorter wavelength and twice the intensity as K2.
The specific wavelengths are characteristic of the target material. Filtering, by foils or crystal
monochrometers, is required to produce monochromatic X-rays needed for diffraction. K1and
K2 are sufficiently close in wavelength such that a weighted average of the two is used.
Molybdenum is the most common target material for single-crystal diffraction, with MoKradiation = 0.7107. These X-rays are collimated and directed onto the sample. When the
geometry of the incident X-rays impinging the sample satisfies the Bragg Equation,constructive interference occurs. A detector records and processes this X-ray signal and
converts the signal to a count rate which is then output to a device such as a printer or
computer monitor. X-rays may also be produced using a synchotron, which emits a much
stronger beam.
Single-crystal diffractometers use either 3- or 4-circle goniometers. These circles refer to
the four angles (2, , , and ) that define the relationship between the crystal lattice, the
incident ray and detector. Samples are mounted on thin glass fibers which are attached to
brass pins and mounted onto goniometer heads. Adjustment of the X, Y and Z orthogonaldirections allows centering of the crystal within the X-ray beam.
X-rays leave the collimator and are directed at the crystal. Rays are either transmitted
through the crystal, reflected off the surface, or diffracted by the crystal lattice. A beam stop
is located directly opposite the collimator to block transmitted rays and prevent burn-out of
the detector. Reflected rays are not picked up by the detector due to the angles involved.
Diffracted rays at the correct orientation for the configuration are then collected by the
detector.Modern single-crystal diffractometers use CCD (charge-coupled device) technology
to transform the X-ray photons into an electrical signal which are then sent to a computer forprocessing.
http://serc.carleton.edu/research_education/geochemsheets/BraggsLaw.htmlhttp://serc.carleton.edu/research_education/geochemsheets/BraggsLaw.htmlhttp://serc.carleton.edu/research_education/geochemsheets/BraggsLaw.html7/30/2019 single crystal XRD1.doc
5/5
Strengths and Limitations of Single-crystal X-ray Diffraction?
Strengths
No separate standards required
Non-destructive
Detailed crystal structure, including unit cell dimensions, bond-lengths, bond-
angles and site-ordering information
Determination of crystal-chemical controls on mineral chemistry
With specialized chambers, structures of high pressure and/or temperature phases
can be determined
Powder patterns can also be derived from single-crystals by use of specialized
cameras (Gandolfi)
Limitations
Must have a single, robust (stable) sample, generally between 50250 microns in
size
Optically clear sample
Twinned samples can be handled with difficulty
Data collection generally requires between 24 and 72 hours