Overview
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 of molecules. X-ray diffraction (XRD) experiments are routinely carried out with either single-crystal or powdered samples.
Single-crystal XRD:
Single-crystal XRD allows for absolute structure determination. With single-crystal XRD data, the exact atomic positions can be observed, and thus bond lengths and angles can be determined. This technique provides the structure within a single crystal, which does not necessarily represent the bulk of the material. Therefore, additional bulk characterization methods must be utilized to prove the identity and purity of a compound.
Powder XRD:
Unlike single-crystal XRD, powder XRD looks at a large sample of polycrystalline material and therefore is considered a bulk characterization technique. The powder pattern is considered a "fingerprint" for a given material; it provides information about the phase (polymorph) and crystallinity of the material. Typically, powder XRD is used to study minerals, zeolites, metal-organic frameworks (MOFs), and other extended solids. Powder XRD can also be used to establish bulk purity of molecular species.
Previously, we have seen how to grow X-ray quality crystals (see video in Essentials of Organic Chemistry series). Here we will learn the principles behind XRD. We will then collect both single-crystal and powder data on Mo2(ArNC(H)NAr)4, where Ar = p-MeOC6H5.
Principles
Why X-rays?:
When measuring distance, it is important to select a unit of measure that is on the scale of the object being measured. For example, to measure the length of a pencil, one would not want to use a yard stick that only has feet gradations. Similarly, if one wanted to measure the length of a car, it would be inappropriate to use a 12-inch ruler with cm marks. Therefore, in order to study bonds in molecules, it is important to use a wavelength of light that matches the length of those bonds. X-rays have wavelengths in the Å range, which matches perfectly with typical bond distances (1-3 Å).
The Unit Cell:
Imagine trying to describe all of the molecules on the tip of a pen. If one approximates that it's comprised of 6.02 × 1023 molecules (or 1 mole), it would seem nearly impossible to describe that object on the molecular level. The complexity of an object is simplified when it exists as a crystal, where the contents of a unit cell can be used to describe the entire structure. The unit cell of a crystal is the least volume containing a repeating unit of a solid. It is defined as a 3D "box" with lengths a, b, and c, and angles α, β, and γ (Figure 1). The unit cell allows chemists to describe the contents of a crystal using a fraction of or a small number of atoms or molecule(s). By repeating the unit cell in space, one can generate a 3D representation of the solid.
Figure 1. Unit cell parameters.
Experimental Setup:
Single-crystal and powder XRD have similar instrumentation setups. For single-crystal XRD, a crystal is mounted and centered within the X-ray beam. For powder XRD, a polycrystalline sample is ground into a fine powder and mounted on a plate. The sample (single- or polycrystalline) is irradiated with X-rays and the diffracted X-rays hit a detector. During data collection, the sample is rotated with respect to the X-ray source and detector.
Double-slit Experiment:
Recall that light has both wave- and particle-like properties. When monochromatic light enters two slits, the wave-like property of light results in light emanating in a spherical fashion from each slit. When the waves interact, they can add together (if the waves have the same wavelength and phase) or cancel each other out (if the waves have the same wavelength, but have different phases), which is called constructive and destructive interference, respectively. The resulting light pattern is made of a series of lines, where the light areas represent constructive interference while the dark areas are a result of destructive interference.
Typical Diffraction Patterns: Single-crystal Versus Powder:
Upon irradiation of a crystal by X-rays, the radiation is diffracted upon interaction with electron density within the crystal. Just like water waves in the classic double-slit experiment from physics, the diffracted X-rays interact, resulting in constructive and destructive interference. In XRD, the diffraction pattern represents the electron density due to atoms and bonds within the crystal. A typical diffraction pattern for a single crystal is shown in (Figure 2). Notice that the diffraction pattern is comprised of spots instead of lines like in the double slit experiment. In fact, these “spots” are 2D slices of 3-dimensional spheres. Crystallographers use a computer program to integrate the resulting spots in order to determine the shape and intensity of the diffracted X-rays. In a powder sample, the X-rays interact with many tiny crystals in random orientations. Therefore, instead of seeing spots, a circular diffraction pattern is observed (Figure 3). The intensities of the diffracted circles are then plotted against the angles between the ring the beam axis (denoted 2θ) to give a 2 dimensional plot known as a powder pattern.
Here, we will collect single crystal and powder XRD data on Mo2(ArNC(H)NAr)4 where Ar = p-MeOC6H5, which was synthesized in the module “Preparation and Characterization of a Quadruply Metal–Metal Bonded Compound.”
Figure 2. Single Crystal Diffraction Pattern.
Figure 3. Powder XRD: Circular Diffraction Pattern.
Procedure
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 2θ between 5-85º 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!
Results
Figure 4. Single-crystal structure of Mo2(ArNC(H)NAr)4 where Ar = p-MeOC6H5.
Figure 5. Powder XRD pattern of Mo2(ArNC(H)NAr)4 where Ar = p-MeOC6H5.
Applications and Summary
In this video, we learned about the difference between single-crystal and powder XRD. We collected both single-crystal and powder data on Mo2(ArNC(H)NAr)4, where Ar = p-MeOC6H5.
Single-crystal XRD is a powerful characterization technique that can provide the absolute structure of a molecule. While structure determination is the most common reason chemists use XRD, there are a variety of special X-ray techniques, such as anomalous scattering and photocrystallography, which provide more information about a molecule.
Anomalous scattering can distinguish between atoms of similar molecular weights. This technique is particularly valuable for characterization of heteropolynuclear metal complexes (compounds that have more than one metal atom with different identities). Anomalous scattering has also been used in protein crystallography as a method to help resolve the phase of the diffracted beam, which is important for structure determination.
Photocrystallography involves single-crystal XRD coupled to photochemistry. By irradiating a sample with light in the solid state, we can observe small structural changes and monitor those changes by XRD. Examples of this technique include observing isomerization of a molecule by light as well as characterization of reactive intermediates.
Powder XRD is a non-destructive characterization method that can be used to gain information about the crystallinity of a sample. In addition, it is a useful technique to analyze mixtures of different materials. As previously mentioned, powder patterns are like fingerprints: the resulting pattern of a compound is dependent on how the atoms are arranged within the material. Therefore, an experimentally-determined powder pattern can be compared to a collection of known diffraction patterns of materials in the International Centre for Diffraction Data. This not only provides information about the identity of the product isolated, but also allows scientists to comment on the number of compounds present in the sample. While a majority of the diffraction patterns listed in the database are in the family of extended solids such as minerals and zeolites, examples of inorganic molecules can be found.
