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69-453: Thus, the two substrates of this enzyme are L-cysteine and [enzyme]-cysteine], whereas its two products are L-alanine and [enzyme]-S-sulfanylcysteine. One group of authors has given it the acronym hapE , for hydrogen sulfide, alanine, and pyruvate producing enzyme. This enzyme belongs to the family of transferases , specifically the sulfurtransferases , which transfer sulfur-containing groups. The systematic name of this enzyme class

138-447: A chemical species being observed in a chemical reaction , or to a surface on which other chemical reactions or microscopy are performed. In the former sense, a reagent is added to the substrate to generate a product through a chemical reaction. The term is used in a similar sense in synthetic and organic chemistry , where the substrate is the chemical of interest that is being modified. In biochemistry , an enzyme substrate

207-443: A neutron beam of suitable intensity and speed for diffraction are only available at a small number of research reactors and spallation sources in the world. Angle dispersive (fixed wavelength) instruments typically have a battery of individual detectors arranged in a cylindrical fashion around the sample holder, and can therefore collect scattered intensity simultaneously on a large 2θ range. Time of flight instruments normally have

276-431: A phase transition . At this point new diffraction peaks will appear or old ones disappear according to the symmetry of the new phase. If the material melts to an isotropic liquid, all sharp lines will disappear and be replaced by a broad amorphous pattern. If the transition produces another crystalline phase, one set of lines will suddenly be replaced by another set. In some cases however lines will split or coalesce, e.g. if

345-408: A crystalline pattern consisting of a series of sharp peaks, amorphous materials (liquids, glasses etc.) produce a broad background signal. Many polymers show semicrystalline behavior, i.e. part of the material forms an ordered crystallite by folding of the molecule. A single polymer molecule may well be folded into two different, adjacent crystallites and thus form a tie between the two. The tie part

414-409: A few others. There are many factors that determine the width B of a diffraction peak. These include: It is often possible to separate the effects of size and strain. When size broadening is independent of q (K = 1/d), strain broadening increases with increasing q-values. In most cases there will be both size and strain broadening. It is possible to separate these by combining the two equations in what

483-456: A given metabolic pathway in clinical DDI studies. Metabolism by the same cytochrome P450 isozyme can result in several clinically significant drug-drug interactions. Powder diffraction Powder diffraction is a scientific technique using X-ray , neutron , or electron diffraction on powder or microcrystalline samples for structural characterization of materials. An instrument dedicated to performing such powder measurements

552-554: A negligible absorption and coherent scattering cross section for neutrons and is hence nearly invisible in a powder diffraction experiment. Vanadium does however have a considerable incoherent scattering cross section which may cause problems for more sensitive techniques such as neutron inelastic scattering. A later development in X-ray cameras is the Guinier camera. It is built around a focusing bent crystal monochromator . The sample

621-458: A particular matrix such as a pharmaceutical tablet, a circuit board, a mechanical weld, a geologic core sampling, cement and concrete, or a pigment found in an historic painting. The method has been historically used for the identification and classification of minerals, but it can be used for nearly any material, even amorphous ones, so long as a suitable reference pattern is known or can be constructed. The most widespread use of powder diffraction

690-578: A piece of X-ray film, now more and more a flat-plate detector or a CCD-camera ) or a cylindrical one (originally a piece of film in a cookie-jar, but increasingly bent position sensitive detectors are used). The two types of cameras are known as the Laue and the Debye–Scherrer camera. In order to ensure complete powder averaging, the capillary is usually spun around its axis. For neutron diffraction vanadium cylinders are used as sample holders. Vanadium has

759-431: A property termed enzyme promiscuity . An enzyme may have many native substrates and broad specificity (e.g. oxidation by cytochrome p450s ) or it may have a single native substrate with a set of similar non-native substrates that it can catalyse at some lower rate. The substrates that a given enzyme may react with in vitro , in a laboratory setting, may not necessarily reflect the physiological, endogenous substrates of

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828-520: A small range of banks at different scattering angles which collect data at varying resolutions. Laboratory X-ray diffraction equipment relies on the use of an X-ray tube , which is used to produce the X-rays . The most commonly used laboratory X-ray tube uses a copper anode, but cobalt and molybdenum are also popular. The wavelength in nm varies for each source. The table below shows these wavelengths, determined by Bearden (all values in nm): According to

897-442: A substrate is called 'fluorogenic' if it gives rise to a fluorescent product when acted on by an enzyme. For example, curd formation ( rennet coagulation) is a reaction that occurs upon adding the enzyme rennin to milk. In this reaction, the substrate is a milk protein (e.g., casein ) and the enzyme is rennin. The products are two polypeptides that have been formed by the cleavage of the larger peptide substrate. Another example

966-415: A whole new phase of development. Not only is there a much wider choice of wavelengths available, the high brilliance of the synchrotron radiation makes it possible to observe changes in the pattern during chemical reactions, temperature ramps, changes in pressure and the like. The tunability of the wavelength also makes it possible to observe anomalous scattering effects when the wavelength is chosen close to

1035-481: Is L-cysteine:[enzyme cysteine] sulfurtransferase. Other names in common use include IscS , NIFS , NifS , SufS , and cysteine desulfurylase . Bacteria contain cysteine desulfurases to form iron sulfur clusters in proteins. However recently it has been shown that the enzyme, which produces hydrogen sulfide from cysteine, is also a virulence factor , namely for M.pneumoniae , in that it causes both α-hemolysis and β-haemolysis of red blood cells. In mammals,

1104-522: Is a combination of the Scherrer equation for size broadening and the Stokes and Wilson expression for strain broadening. The value of η is the strain in the crystallites, the value of D represents the size of the crystallites. The constant k is typically close to unity and ranges from 0.8 to 1.39. X-ray photons scatter by interaction with the electron cloud of the material, neutrons are scattered by

1173-429: Is a far more powerful technique for structure determination. This is directly related to the fact that information is lost by the collapse of the 3D space onto a 1D axis. Nevertheless, powder X-ray diffraction is a powerful and useful technique in its own right. It is mostly used to characterize and identify phases , and to refine details of an already known structure, rather than solving unknown structures. Advantages of

1242-406: Is called a powder diffractometer . Powder diffraction stands in contrast to single crystal diffraction techniques, which work best with a single, well-ordered crystal. The most common type of powder diffraction is with X-rays , the focus of this article although some aspects of neutron powder diffraction are mentioned. (Powder electron diffraction is more complex due to dynamical diffraction and

1311-538: Is extremely challenging due to the overlap of reflections in a powder experiment. A number of different methods exist for structural determination, such as simulated annealing and charge flipping. The crystal structures of known materials can be refined, i.e. as a function of temperature or pressure, using the Rietveld method . The Rietveld method is a so-called full pattern analysis technique. A crystal structure, together with instrumental and microstructural information,

1380-403: Is homogeneous over φ * and χ *, and only q remains as an important measurable quantity. This is because orientational averaging causes the three-dimensional reciprocal space that is studied in single crystal diffraction to be projected onto a single dimension. When the scattered radiation is collected on a flat plate detector, the rotational averaging leads to smooth diffraction rings around

1449-439: Is in the identification and characterization of crystalline solids, each of which produces a distinctive diffraction pattern. Both the positions (corresponding to lattice spacings) and the relative intensity of the lines in a diffraction pattern are indicative of a particular phase and material, providing a "fingerprint" for comparison. A multi-phase mixture, e.g. a soil sample, will show more than one pattern superposed, allowing for

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1518-453: Is independent of the atomic positions within the cell and entirely determined by the size and shape of the unit cell of the crystalline phase. Each peak represents a certain lattice plane and can therefore be characterized by a Miller index . If the symmetry is high, e.g.: cubic or hexagonal it is usually not too hard to identify the index of each peak, even for an unknown phase. This is particularly important in solid-state chemistry , where one

1587-522: Is interested in finding and identifying new materials. Once a pattern has been indexed, this characterizes the reaction product and identifies it as a new solid phase. Indexing programs exist to deal with the harder cases, but if the unit cell is very large and the symmetry low (triclinic) success is not always guaranteed. Cell parameters are somewhat temperature and pressure dependent. Powder diffraction can be combined with in situ temperature and pressure control. As these thermodynamic variables are changed,

1656-632: Is known as the Hall–Williamson method: Thus, when we plot B ⋅ cos ⁡ ( θ ) {\displaystyle \displaystyle B\cdot \cos(\theta )} vs. sin ⁡ ( θ ) {\displaystyle \displaystyle \sin(\theta )} we get a straight line with slope η {\displaystyle \displaystyle \eta } and intercept k λ D {\displaystyle \displaystyle {\frac {k\lambda }{D}}} . The expression

1725-482: Is more common. The powder sample is loaded in a small disc-like container and its surface carefully flattened. The disc is put on one axis of the diffractometer and tilted by an angle θ while a detector ( scintillation counter ) rotates around it on an arm at twice this angle. This configuration is known under the name Bragg–Brentano θ -2 θ . Another configuration is the Bragg–Brentano θ - θ configuration in which

1794-751: Is not an endogenous, in vivo substrate for FAAH. In another example, the N -acyl taurines (NATs) are observed to increase dramatically in FAAH-disrupted animals, but are actually poor in vitro FAAH substrates. Sensitive substrates also known as sensitive index substrates are drugs that demonstrate an increase in AUC of ≥5-fold with strong index inhibitors of a given metabolic pathway in clinical drug-drug interaction (DDI) studies. Moderate sensitive substrates are drugs that demonstrate an increase in AUC of ≥2 to <5-fold with strong index inhibitors of

1863-406: Is not discussed further herein.) Typical diffractometers use electromagnetic radiation (waves) with known wavelength and frequency, which is determined by their source. The source is often X-rays , and neutrons are also common sources, with their frequency determined by their de Broglie wavelength . When these waves reach the sample, the incoming beam is either reflected off the surface, or can enter

1932-408: Is prevented from crystallizing. The result is that the crystallinity will never reach 100%. Powder XRD can be used to determine the crystallinity by comparing the integrated intensity of the background pattern to that of the sharp peaks. Values obtained from powder XRD are typically comparable but not quite identical to those obtained from other methods such as DSC . The position of a diffraction peak

2001-468: Is represented equally in a powdered sample, the isotropic case. Powder X-ray diffraction (PXRD) operates under the assumption that the sample is randomly arranged. Therefore, a statistically significant number of each plane of the crystal structure will be in the proper orientation to diffract the X-rays. Therefore, each plane will be represented in the signal. In practice, it is sometimes necessary to rotate

2070-400: Is shown as a function either of the scattering angle 2 θ or as a function of the scattering vector length q . The latter variable has the advantage that the diffractogram no longer depends on the value of the wavelength λ . The advent of synchrotron sources has widened the choice of wavelength considerably. To facilitate comparability of data obtained with different wavelengths the use of q

2139-470: Is shown in the figure, where K 0 and K stand for the wave vectors of the incoming and diffracted beam that both make up the scattering plane. Various other settings for texture or stress/strain measurements can also be visualized with this graphical approach. Position-sensitive detectors (PSD) and area detectors, which allow collection from multiple angles at once, are becoming more popular on currently supplied instrumentation. Sources that produce

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2208-427: Is the chemical decomposition of hydrogen peroxide carried out by the enzyme catalase . As enzymes are catalysts , they are not changed by the reactions they carry out. The substrate(s), however, is/are converted to product(s). Here, hydrogen peroxide is converted to water and oxygen gas. While the first (binding) and third (unbinding) steps are, in general, reversible , the middle step may be irreversible (as in

2277-405: Is the material upon which an enzyme acts. When referring to Le Chatelier's principle , the substrate is the reagent whose concentration is changed. In the latter sense, it may refer to a surface on which other chemical reactions are performed or play a supporting role in a variety of spectroscopic and microscopic techniques, as discussed in the first few subsections below. In three of

2346-557: Is therefore one of the most powerful methods to identify and characterize new materials in this field. Particularly for neutron diffraction , which requires larger samples than X-ray diffraction due to a relatively weak scattering cross section , the ability to use large samples can be critical, although newer and more brilliant neutron sources are being built that may change this picture. Since all possible crystal orientations are measured simultaneously, collection times can be quite short even for small and weakly scattering samples. This

2415-459: Is therefore recommended and gaining acceptability. Relative to other methods of analysis, powder diffraction allows for rapid, non-destructive analysis of multi-component mixtures without the need for extensive sample preparation. This gives laboratories the ability to quickly analyze unknown materials and perform materials characterization in such fields as metallurgy, mineralogy, chemistry, forensic science, archeology, condensed matter physics, and

2484-476: Is used to generate a theoretical diffraction pattern that can be compared to the observed data. A least squares procedure is then used to minimize the difference between the calculated pattern and each point of the observed pattern by adjusting model parameters. Techniques to determine unknown structures from powder data do exist, but are somewhat specialized. A number of programs that can be used in structure determination are TOPAS, Fox, DASH, GSAS-II, EXPO2004, and

2553-620: Is usually placed in the focusing beam, e.g. as a dusting on a piece of sticky tape. A cylindrical piece of film (or electronic multichannel detector) is put on the focusing circle, but the incident beam prevented from reaching the detector to prevent damage from its high intensity. Cameras based on hybrid photon counting technology , such as the PILATUS detector , are widely used in applications where high data acquisition speeds and increased data quality are required. Diffractometers can be operated both in transmission and reflection, but reflection

2622-474: The absorption edge of one of the elements of the sample. Neutron diffraction has never been an in house technique because it requires the availability of an intense neutron beam only available at a nuclear reactor or spallation source. Typically the available neutron flux, and the weak interaction between neutrons and matter, require relative large samples. Although it is possible to solve crystal structures from powder X-ray data alone, its single crystal analogue

2691-505: The background in the diffraction pattern. A notorious example is the presence of iron in a sample when using copper radiation. In general elements just below the anode element in the period system need to be avoided. Another limitation is that the intensity of traditional generators is relatively low, requiring lengthy exposure times and precluding any time dependent measurement. The advent of synchrotron sources has drastically changed this picture and caused powder diffraction methods to enter

2760-406: The beam axis, rather than the discrete Laue spots observed in single crystal diffraction. The angle between the beam axis and the ring is called the scattering angle and in X-ray crystallography always denoted as 2 θ (in scattering of visible light the convention is usually to call it θ ). In accordance with Bragg's law , each ring corresponds to a particular reciprocal lattice vector G in

2829-577: The biological and pharmaceutical sciences. Identification is performed by comparison of the diffraction pattern to a known standard or to a database such as the International Centre for Diffraction Data 's Powder Diffraction File (PDF) or the Cambridge Structural Database (CSD). Advances in hardware and software, particularly improved optics and fast detectors, have dramatically improved the analytical capability of

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2898-410: The case of more than one substrate, these may bind in a particular order to the active site, before reacting together to produce products. A substrate is called 'chromogenic' if it gives rise to a coloured product when acted on by an enzyme. In histological enzyme localization studies, the colored product of enzyme action can be viewed under a microscope, in thin sections of biological tissues. Similarly,

2967-550: The case of neutron scattering from hydrogenous materials is the strong incoherent scattering of hydrogen (80.27(6) barn ). This leads to a very high background in neutron diffraction experiments, and may make structural investigations impossible. A common solution is deuteration, i.e., replacing the 1-H atoms in the sample with deuterium (2-H). The incoherent scattering length of deuterium is much smaller (2.05(3) barn) making structural investigations significantly easier. However, in some systems, replacing hydrogen with deuterium may alter

3036-528: The determination of the relative concentrations of phases in the mixture. J.D. Hanawalt, an analytical chemist who worked for Dow Chemical in the 1930s, was the first to realize the analytical potential of creating a database. Today it is represented by the Powder Diffraction File (PDF) of the International Centre for Diffraction Data (formerly Joint Committee for Powder Diffraction Studies). This has been made searchable by computer through

3105-510: The effect of nano-crystallite shape on detected diffraction peaks, even if in some directions the cluster is only one atom thick. Semi-quantitative analysis of polycrystalline mixtures can be performed by using traditional single-peaks methods such as the Relative Intensity Ratio (RIR) or whole-pattern methods using Rietveld Refinement or PONCKS (Partial Or No Known Crystal Structures) method. The use of each method depends on

3174-465: The enzyme participates in thiamine metabolism . As of late 2007, only one structure had been solved for this class of enzymes, with the PDB accession code 1T3I . This EC 2.8 enzyme -related article is a stub . You can help Misplaced Pages by expanding it . Substrate (biochemistry) In chemistry , the term substrate is highly context-dependent. Broadly speaking, it can refer either to

3243-432: The enzyme's reactions in vivo . That is to say that enzymes do not necessarily perform all the reactions in the body that may be possible in the laboratory. For example, while fatty acid amide hydrolase (FAAH) can hydrolyze the endocannabinoids 2-arachidonoylglycerol (2-AG) and anandamide at comparable rates in vitro , genetic or pharmacological disruption of FAAH elevates anandamide but not 2-AG, suggesting that 2-AG

3312-471: The intersections where the waves are out of phase, and do not lead to bright spots in the diffraction pattern. Because the sample itself is acting as the diffraction grating, this spacing is the atomic spacing. The distinction between powder and single crystal diffraction is the degree of texturing in the sample. Single crystals have maximal texturing, and are said to be anisotropic . In contrast, in powder diffraction, every possible crystalline orientation

3381-406: The knowledge on the analyzed system, given that, for instance, Rietveld refinement needs the solved crystal structure of each component of the mixture to be performed. In the last decades, multivariate analysis begun spreading as an alternative method for phase quantification. The simplest cameras for X-ray powder diffraction consist of a small capillary and either a flat plate detector (originally

3450-514: The last re-examination of Hölzer et al. (1997), and quoted in the International Tables for Crystallography these values are respectively: In-house applications of X-ray diffraction has always been limited to the relatively few wavelengths shown in the table above. The available choice was much needed because the combination of certain wavelengths and certain elements present in a sample can lead to strong fluorescence which increases

3519-411: The lattice and be diffracted by the atoms present in the sample. If the atoms are arranged symmetrically with a separation distance d , these waves will interfere constructively only where the path-length difference 2 d  sin  θ is equal to an integer multiple of the wavelength, producing a diffraction maximum in accordance with Bragg's law . These waves interfere destructively at points between

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3588-477: The material undergoes a continuous, second order phase transition. In such cases the symmetry may change because the existing structure is distorted rather than replaced by a completely different one. For example, the diffraction peaks for the lattice planes (100) and (001) can be found at two different values of q for a tetragonal phase, but if the symmetry becomes cubic the two peaks will come to coincide. Crystal structure determination from powder diffraction data

3657-553: The microscopy data. Samples are deposited onto the substrate in fine layers where it can act as a solid support of reliable thickness and malleability. Smoothness of the substrate is especially important for these types of microscopy because they are sensitive to very small changes in sample height. Various other substrates are used in specific cases to accommodate a wide variety of samples. Thermally-insulating substrates are required for AFM of graphite flakes for instance, and conductive substrates are required for TEM. In some contexts,

3726-408: The most common nano-scale microscopy techniques, atomic force microscopy (AFM), scanning tunneling microscopy (STM), and transmission electron microscopy (TEM), a substrate is required for sample mounting. Substrates are often thin and relatively free of chemical features or defects. Typically silver, gold, or silicon wafers are used due to their ease of manufacturing and lack of interference in

3795-645: The nuclei. This means that, in the presence of heavy atoms with many electrons, it may be difficult to detect light atoms by X-ray diffraction. In contrast, the neutron scattering lengths of most atoms are approximately equal in magnitude. Neutron diffraction techniques may therefore be used to detect light elements such as oxygen or hydrogen in combination with heavy atoms. The neutron diffraction technique therefore has obvious applications to problems such as determining oxygen displacements in materials like high temperature superconductors and ferroelectrics, or to hydrogen bonding in biological systems. A further complication in

3864-467: The observed diffraction peaks will migrate continuously to indicate higher or lower lattice spacings as the unit cell distorts. This allows for measurement of such quantities as the thermal expansion tensor and the isothermal bulk modulus , as well determination of the full equation of state of the material. At some critical set of conditions, for example 0 °C for water at 1 atm, a new arrangement of atoms or molecules may become stable, leading to

3933-413: The reaction of interest, but they frequently bind the reagents with some affinity to allow sticking to the substrate. The substrate is exposed to different reagents sequentially and washed in between to remove excess. A substrate is critical in this technique because the first layer needs a place to bind to such that it is not lost when exposed to the second or third set of reagents. In biochemistry ,

4002-476: The rennin and catalase reactions just mentioned) or reversible (e.g. many reactions in the glycolysis metabolic pathway). By increasing the substrate concentration, the rate of reaction will increase due to the likelihood that the number of enzyme-substrate complexes will increase; this occurs until the enzyme concentration becomes the limiting factor . Although enzymes are typically highly specific, some are able to perform catalysis on more than one substrate,

4071-552: The resulting data collection. Silicon substrates are also commonly used because of their cost-effective nature and relatively little data interference in X-ray collection. Single-crystal substrates are useful in powder diffraction because they are distinguishable from the sample of interest in diffraction patterns by differentiating by phase. In atomic layer deposition , the substrate acts as an initial surface on which reagents can combine to precisely build up chemical structures. A wide variety of substrates are used depending on

4140-409: The sample crystal. This leads to the definition of the scattering vector as: In this equation, G is the reciprocal lattice vector, q is the length of the reciprocal lattice vector, k is the momentum transfer vector, θ is half of the scattering angle, and λ is the wavelength of the source. Powder diffraction data are usually presented as a diffractogram in which the diffracted intensity, I ,

4209-493: The sample is stationary while the X-ray tube and the detector are rotated around it. The angle formed between the X-ray source and the detector is 2 θ . This configuration is most convenient for loose powders. Diffractometer settings for different experiments can schematically be illustrated by a hemisphere, in which the powder sample resides in the origin. The case of recording a pattern in the Bragg-Brentano θ - θ mode

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4278-574: The sample orientation to eliminate the effects of texturing and achieve true randomness. Mathematically, crystals can be described by a Bravais lattice with some regularity in the spacing between atoms. Because of this regularity, we can describe this structure in a different way using the reciprocal lattice , which is related to the original structure by a Fourier transform . This three-dimensional space can be described with reciprocal axes x *, y *, and z * or alternatively in spherical coordinates q , φ *, and χ *. In powder diffraction, intensity

4347-453: The solid state is (to first order) done rather elegantly with the Debye scattering equation: where the magnitude of the scattering vector q is in reciprocal lattice distance units, N is the number of atoms, f i ( q ) is the atomic scattering factor for atom i and scattering vector q , while r ij is the distance between atom i and atom j . One can also use this to predict

4416-511: The structural and dynamic properties of interest. As neutrons also have a magnetic moment, they are additionally scattered by any magnetic moments in a sample. In the case of long range magnetic order, this leads to the appearance of new Bragg reflections. In most simple cases, powder diffraction may be used to determine the size of the moments and their spatial orientation. Predicting the scattered intensity in powder diffraction patterns from gases, liquids, and randomly distributed nano-clusters in

4485-431: The substrate is a molecule upon which an enzyme acts. Enzymes catalyze chemical reactions involving the substrate(s). In the case of a single substrate, the substrate bonds with the enzyme active site , and an enzyme-substrate complex is formed. The substrate is transformed into one or more products , which are then released from the active site. The active site is then free to accept another substrate molecule. In

4554-547: The technique are: By contrast growth and mounting of large single crystals is notoriously difficult. In fact there are many materials for which, despite many attempts, it has not proven possible to obtain single crystals. Many materials are readily available with sufficient microcrystallinity for powder diffraction, or samples may be easily ground from larger crystals. In the field of solid-state chemistry that often aims at synthesizing new materials, single crystals thereof are typically not immediately available. Powder diffraction

4623-459: The technique, especially relative to the speed of the analysis. The fundamental physics upon which the technique is based provides high precision and accuracy in the measurement of interplanar spacings, sometimes to fractions of an Ångström , resulting in authoritative identification frequently used in patents, criminal cases and other areas of law enforcement. The ability to analyze multiphase materials also allows analysis of how materials interact in

4692-436: The word substrate can be used to refer to the sample itself, rather than the solid support on which it is placed. Various spectroscopic techniques also require samples to be mounted on substrates, such as powder diffraction . This type of diffraction, which involves directing high-powered X-rays at powder samples to deduce crystal structures, is often performed with an amorphous substrate such that it does not interfere with

4761-545: The work of global software developers and equipment manufacturers. There are now over 1,047,661 reference materials in the 2021 Powder Diffraction File Databases, and these databases are interfaced to a wide variety of diffraction analysis software and distributed globally. The Powder Diffraction File contains many subfiles, such as minerals, metals and alloys, pharmaceuticals, forensics, excipients, superconductors, semiconductors, etc., with large collections of organic, organometallic and inorganic reference materials. In contrast to

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