How Do Crystallography Instruments Work?
Crystallography is one of the most important techniques for Mineralogy, Physics, Chemistry, Biology and Biomedicine. It has revolutionized our knowledge of the structure of inorganic molecules and also of proteins and other biological macromolecules.
Data processing starts with indexation, which determines the dimensions and symmetry of the unit cell and assigns image peak positions to points in reciprocal space. This information is then converted to intensity data for each reflection.
X-ray crystallography depends on the structure of crystalline materials and compounds. This structural information is determined by measuring diffraction patterns of the compound. The patterns are compared with patterns from reference databases to identify the molecular structure and chemical formula. The process is similar to matching fingerprints in a crime scene investigation.
The first step in the X-ray crystallography process is to find suitable crystals. The crystals are then frozen in liquid nitrogen and taken to a synchrotron, which is a large machine that accelerates electrically charged particles, such as electrons, to nearly the speed of light. The electrons then collide with a target material, which emits X-rays, such as photons and bremsstrahlung.
The resulting diffraction pattern is recorded on a detector, where the intensity of the X-rays is measured. A peak in the diffraction pattern occurs when an atomic plane in the crystal diffracts the X-ray beam at a specific angle, known as the Bragg angle. This is determined using the Bragg equation, which states that a beam of X-rays must reflect off of a number of evenly spaced atomic planes to produce a reinforced diffraction pattern.
X-ray diffraction systems
X-ray crystallography involves measuring the intensity of a pattern of reflections that is produced when an incident X-ray beam strikes a crystal. This data is combined computationally with complementary chemical information to produce and refine a model of the atomic arrangement within a crystal. The result is a 3D structural model.
This model is based on Bragg’s law, which states that each crystallographic reflection is associated with evenly spaced planes in the crystal lattice. The resulting structure can be used to predict the location of individual atoms in a given crystal.
Other X-ray scattering methods include powder diffraction and small-angle X-ray scattering (SAXS). The latter is often used to study self-assembled systems, such as block copolymers, that have periodic order but with repeat distances significantly larger than those of a single molecule.
A typical X-ray crystallography system includes an X-ray source, a sample holder and an X-ray detector. Several images of the sample are collected in different orientations and the relative intensities of the corresponding diffraction peaks are recorded using photographic film or area detectors, such as charge-coupled device (CCD) image sensors.
In X-ray crystallography, a single-crystal diffraction pattern is used to determine the arrangement of atoms in the crystal lattice. These arrangements are characterized by a series of mathematical calculations. The diffraction pattern is then recorded on an image plate detector, a scintillator crystal that converts X-rays into visible light, or on a charged-coupled device (CCD) sensor. The diffraction data is then used to construct an image of the structure.
X-rays are usually filtered and collimated to a single direction before they are allowed to strike the sample. This makes data collection more efficient. It also reduces the number of photons that degrade the crystal without contributing useful information. The collimation is often achieved by using a three- or four-circle goniometer.
The diffraction patterns can be assigned indices (hkl) that describe the spatial relationship between them. This information can then be combined with chemical information to produce a model of the crystal’s atomic arrangement. This is called single-crystal X-ray structure refinement.
X-ray spectrometers are used to measure the atomic composition of crystal samples. They work by passing an X-ray beam through the sample, causing it to ionize and release energy. This energy is measured in the form of characteristic X-ray wavelengths, which indicate the types of atoms present in the sample.
The X-ray beam is typically filtered to make it monochromatic, and it is collimated to ensure that the diffraction pattern is centered on the crystal. This can be done with a simple Soller collimator, or with a complex arrangement of mirrors. The diffraction pattern is recorded on a detector, and the intensity is measured using either a gas flow proportional counter or a scintillation detector.
A full data set can consist of hundreds of images, which must be merged and scaled to create a consistent intensity scale. This process is important, as the intensity of diffraction spots indicates the electron density of the sample. The data is then compared to the known structure of the molecule.