Single Crystal and Powder X-ray Diffraction
Source: Tamara M. Powers, Department of Chemistry, Texas A&M University
X-ray crystallography is a technique that uses X-rays to study the structure o…
1. Collecting Single Crystal XRD Data
- Grow suitable crystals for XRD. For more information, please see videos "Growing Crystals for X-ray Diffraction Analysis" in the Essentials of Organic Chemistry series and "Preparation and Characterization of a Quadruply Metal-Metal Bonded Compound" in the Inorganic Chemistry series.
- Add a drop of paratone oil to a glass slide. Using a spatula and a small amount of paratone oil, scoop some crystals from the vial used to grow the crystals and add them to the drop of oil on the slide.
- Under a microscope, select a crystal that has uniform, well-defined edges.
- Pick up the selected crystal using a suitable mount (here we use a Kapton loop). Make sure that there that any oil stuck to the crystal is minimal once it is mounted.
- Open the instrument doors.
- Attach the mount to the goniometer head on the instrument.
- Center the crystal with respect to the location of the X-ray beam.
- Close the instrument doors.
- Open the APEX3 software suite, a graphical user interface (GUI) for X-ray crystallography.
- Run a short data collection sequence and determine the unit cell.
- Based on the unit cell data, pick a data collection strategy and run a full data collection.
- Workup the data using a suitable program. Here we use SHELX in the APEX 3 suite.
- Refine the structure in a suitable GUI. Here we use SHELX in OLEX2.
2. Loading a Powder Sample onto the Sample Holder for Powder XRD
NOTE: Here we will use a Si crystal zero background holder. There are a variety of alternate sample holders that can accommodate different amounts of material. The Si crystal zero background holder produces no background noise from 20-120 ° (2 θ, using Cu radiation).
- Place a fine mesh sieve above the Si crystal.
- Pour approximately 20 mg of the sample onto the sieve, making sure that most of the sample is directly above the Si crystal on the mount.
- Tap the sieve on the bench top until a monolayer of sample covers the Si crystal surface.
- Unscrew the sample holder and place the crystal in the holder.
3. Collecting a Powder XRD Pattern
- Open the instrument doors.
- Mount the sample holder in the instrument.
- Open the Commander software suite (a program used to collect powder XRD patterns).
- In the "Wizard" tab, load a standard data collection scan.
- Select the amount of time to run the scan (20 min). Running a longer scan over the same angle range will generate a better resolved powder XRD pattern.
- Select the angle range (2 θ) that will be scanned (5-70 °). The angle range selected depends on the material. The wavelength range given here is appropriate for molecular inorganic materials.
- Hit the "start" button to start data collection.
X-ray diffraction is a common analytical technique used in materials science and biochemistry to determine the structures of crystals.
It traces the paths of X-rays through crystals to probe the structure. There are two major techniques. Powder X-ray diffraction determines the phases and purity of a crystalline species. Single X-ray diffraction identifies the atoms in a crystal and their locations, as well as electron densities, bond lengths, and angles.
This video illustrates the operation of an X-ray diffractometer, procedures for both single-crystal and powder X-ray diffraction, and discusses a few applications.
We'll start by examining the concept of crystal structure, and exploring how X-rays interact with crystals.
A crystal is a periodic configuration of atoms, that is, a geometric pattern of atoms that repeat at regular intervals. The smallest repeating element of a crystal is called a "unit cell." It is described by its packing structure, dimensions and bond angles. "Miller indices" describe any fictitious planar cross sections of the unit cell.
X-rays are a form of electromagnetic waves whose wavelengths are similar to the atomic spacing in crystals. When a single X-ray strikes an individual atom, it is diffracted. When two coherent X-rays strike atoms in different planes, the diffracted X-rays interfere, resulting in constructive or destructive signals.
The diffraction pattern of a powder crystalline sample is comprised of intense spots, which form rings of constructive interference. The angles at which these spots occur correspond to the spacing of atoms in that plane. The spacing can be determined using Bragg's Law.
Now that we have learned about crystals and X-ray diffraction patterns, let's look at how an X-ray diffractometer works.
An X-ray diffractometer consists of three basic components: an X-ray source, a specimen, and a detector. All components are oriented in a coplanar, circular arrangement with the sample holder at the center. The source usually contains a copper target, that, when bombarded by electrons, emits a beam of collimated X-rays. The beam is directed at the sample, which refracts the X-rays. The sample and the detector are then rotated in opposite directions, until the angles of X-ray intensity are determined.
High X-ray intensity corresponds to constructive interference by a crystallographic plane in both single-crystal and powder X-ray diffraction. Powder X-ray diffraction reveals the crystal structure of the sample, while single-crystal X-ray diffraction additionally reveals the chemical content and locations of atoms.
Now, let us see a practical example of X-ray diffractometry.
Single-crystal X-ray diffraction requires high-quality crystals without impurities, grain boundaries, or other interfacial defects. Bring the crystals of the organo-molybdenum compound to the light microscope to analyze it.
Begin by adding a drop of paratone oil to a clean glass slide. Then add a small amount of paratone oil to a spatula, and scoop some crystals from the crystallization vial onto a slide.
Examine the crystals under the microscope, and select a crystal with uniform, well defined edges. Once an ideal crystal is chosen, use a Kapton loop to pick up the crystal, ensuring little oil sticks to the crystal.
Next, open the diffractometer doors to load the sample. Attach the Kapton loop to the gonoimeter head, centering the crystal with respect to the X-ray beam. Then close the doors.
Open the X-ray crystallography software and run a short data collection sequence that establishes the structure of the unit cell. Based on this data, select a data collection strategy and run full data collection. Once a full data set has been collected, work up the data using a suitable program and refine it.
In comparison to single crystal X-ray diffraction, powder X-ray diffraction is a bulk characterization technique that does not require single crystals.
Choose an appropriately-sized sample holder and a diffraction plate that will not affect the readings at the angles of interest.
Place a fine mesh sieve over the diffraction plate. Carefully add 20 mg of sample to the sieve, keeping the sample over the plate. Tap the sieve on the benchtop until a monolayer of powder forms.
Secure the diffraction plate in the sample holder. Open the diffractometer doors and mount the sample. If the sample mount has locking pins, ensure the pins are engaged and the sample holder is secure before closing the doors.
Using a suitable software, load a standard data collection method. Enter a range of scan angles suitable for the material. Then enter the scan time; a longer scan time allows for better resolution. Then press "start".
Now, let's compare the results obtained from the single crystal and powder X-ray diffraction of the organo-molybdenum complex.
From the single crystal X-ray data, a structural model of the electron density map is generated, which is used to obtain experimentally determined bond lengths and angles within the structure.
Furthermore, the powder XRD provides additional information about the compound. The flat baseline of the spectrum indicates, that the sample used is highly crystalline, whereas curved baselines are indicative of amorphous materials.
X-ray diffraction is a valuable characterization tool in virtually every field of material science, and therefore plays a role in diverse applications.
A major component of heritage art conservation includes understanding how works of art were produced and why they corrode. Recent developments in X-ray diffraction study corrosion by destructively testing less than 1 mg of sample. Since corrosion products are rarely monocrystalline, powder X-ray diffraction is required. Typical analyses occur at 2? between 5-85? degrees over 20 hours. The locations of atoms within the crystal may be optimized algorithmically, providing insight into the location and nature of chemical attacks.
Films of material ranging from nanometers to micrometers in thickness have unique protective, electrical, and optical abilities that differ from those of bulk materials. X-ray diffraction provides information on film thickness, density, and surface texture. It is used to determine film stress, and the likelihood of film failure and breakage. It also helps characterize the optical behavior of films, since absorption largely depends on crystal structure. It is therefore used to characterize thin film light sensors and photovoltaic cells.
You've just watched JoVE's introduction to single-crystal and powder X-ray diffraction. You should now be familiar with the principles of X-ray diffractometry, a procedure for obtaining diffraction patterns, and some applications. As always, thanks for watching!
Q1: What is the difference between single-crystal and powder X-ray diffraction?
Single-crystal X-ray diffraction identifies atomic positions, bond lengths, and angles within a crystal structure. Powder X-ray diffraction is a bulk characterization technique that determines phases, purity, and crystallinity of polycrystalline materials without requiring high-quality single crystals. Powder patterns serve as fingerprints for identifying materials.
Q2: How does Bragg's Law relate to X-ray diffraction patterns?
Bragg's Law determines the spacing of atoms in crystal planes by analyzing the angles at which intense diffraction spots occur. When X-rays strike atoms in different planes, they interfere constructively or destructively. The angles of constructive interference correspond directly to atomic plane spacing, allowing researchers to calculate crystal structure parameters.
Q3: What are the main components of an X-ray diffractometer?
An X-ray diffractometer consists of three basic components: an X-ray source containing a copper target that emits collimated X-rays, a specimen holder at the center of a coplanar circular arrangement, and a detector. The sample and detector rotate in opposite directions to determine angles of X-ray intensity corresponding to constructive interference.
Q4: Why must single-crystal X-ray diffraction samples meet specific quality requirements?
Single-crystal X-ray diffraction requires high-quality crystals without impurities, grain boundaries, or interfacial defects to accurately determine atomic positions and electron densities. Defects scatter X-rays unpredictably, degrading data quality. Researchers select crystals with uniform, well-defined edges under a microscope and use techniques like Kapton loops to minimize contamination during sample preparation.
Q5: How does X-ray diffraction help characterize thin films and photovoltaic materials?
X-ray diffraction provides information on film thickness, density, surface texture, and stress in thin films ranging from nanometers to micrometers. Since optical behavior depends on crystal structure, X-ray diffraction characterizes dye sensitized solar cells principle fabrication and performance by revealing how absorption relates to crystallinity, helping predict film failure and optimize light-sensing capabilities.
Q6: What information can powder X-ray diffraction provide about sample crystallinity?
A flat baseline in a powder X-ray diffraction spectrum indicates a highly crystalline sample, while curved baselines suggest amorphous materials. This visual distinction allows researchers to quickly assess sample quality and crystalline order without requiring single crystals, making powder diffraction ideal for bulk characterization of minerals, zeolites, and other extended solids.
Q7: How is powder X-ray diffraction applied in heritage art conservation?
Powder X-ray diffraction studies corrosion in artworks by destructively testing less than 1 mg of sample, revealing how and why artworks corrode. Since corrosion products are rarely monocrystalline, powder diffraction is required. Typical analyses scan between 5-85 degrees over 20 hours, allowing researchers to algorithmically optimize atomic locations and understand the nature of chemical attacks on materials.