text
stringlengths 107
11k
| label
int64 0
1
| label_text
stringclasses 2
values |
|---|---|---|
:Direct methods in crystallography are a collection of mathematical techniques that seek to determine crystal structure based on measurements of diffraction patterns and potentially other a priori knowledge (constraints). The central challenge of inverting measured diffraction intensities (i.e. applying an inverse Fourier Transform) to determine the original crystal potential is that phase information is lost in general since intensity is a measurement of the square of the modulus of the amplitude of any given diffracted beam. This is known as the phase problem of crystallography.
:If the diffraction can be considered kinematical, constraints may be used to probabilistically relate the phases of the reflections to their amplitudes, and the original structure can be solved via direct methods (see Sayre equation as an example). Kinematical diffraction is often the case in x-ray diffraction, and is one of the primary reasons that technique has been so successful at solving crystal structures. However, in electron diffraction, the probing wave interacts much more strongly with the electrostatic crystal potential, and complex dynamical diffraction effects can dominate the measured diffraction patterns. This makes application of direct methods much more challenging without a priori knowledge of the structure in question. | 1 | Crystallography |
*[http://www-ssrl.slac.stanford.edu/absorb.html The SSRL Absorption Package] —
*[https://web.archive.org/web/20081223025616/http://www.gwyndafevans.co.uk/chooch.html CHOOCH] —
*[https://web.archive.org/web/20090909133542/http://www.hwi.buffalo.edu/snb/ Shake-and-Bake] (SnB) —
*[http://shelx.uni-ac.gwdg.de/SHELX/ SHELX] — | 1 | Crystallography |
To a known volume of sample, an excess but known amount of I is added, which the oxidizing agent then oxidizes to I. I dissolves in the iodide-containing solution to give triiodide ions (I), which have a dark brown color. The triiodide ion solution is then titrated against standard thiosulfate solution to give iodide again using starch indicator:
: (E = +0.54 V)
Together with reduction potential of thiosulfate:
: (E = +0.08 V)
The overall reaction is thus:
: (E = +0.46 V)
For simplicity, the equations will usually be written in terms of aqueous molecular iodine rather than the triiodide ion, as the iodide ion did not participate in the reaction in terms of mole ratio analysis. The disappearance of the deep blue color is, due to the decomposition of the iodine-starch clathrate, marks the end point.
The reducing agent used does not necessarily need to be thiosulfate; stannous chloride, sulfites, sulfides, arsenic(III), and antimony(III) salts are commonly used alternatives at pH above 8.
At low pH, the following reaction might occur with thiosulfate:
Some reactions involving certain reductants are reversible at certain pH, thus the pH of the sample solution should be carefully adjusted before performing the analysis. For example, the reaction:
is reversible at pH below 4.
The volatility of iodine is also a source of error for the titration, this can be effectively prevented by ensuring an excess iodide is present and cooling the titration mixture. Strong light, nitrite and copper ions catalyse the conversion of iodide to iodine, so these should be removed prior to the addition of iodide to the sample.
For prolonged titrations, it is advised to add dry ice to the titration mixture to displace air from the Erlenmeyer flask so as to prevent the aerial oxidation of iodide to iodine. Standard iodine solution is prepared from potassium iodate and potassium iodide, which are both primary standards:
Iodine in organic solvents, such as diethyl ether and carbon tetrachloride, may be titrated against sodium thiosulfate dissolved in acetone. | 0 | Chromatography + Titration + pH indicators |
The main use of litmus is to test whether a solution is acidic or basic, as blue litmus paper turns red under acidic conditions, and red litmus paper turns blue under basic or alkaline conditions, with the color change occurring over the pH range 4.5–8.3 at . Neutral litmus paper is purple. Wet litmus paper can also be used to test for water-soluble gases that affect acidity or basicity; the gas dissolves in the water and the resulting solution colors the litmus paper. For instance, ammonia gas, which is alkaline, turns red litmus paper blue. While all litmus paper acts as pH paper, the opposite is not true.
Litmus can also be prepared as an aqueous solution that functions similarly. Under acidic conditions, the solution is red, and under alkaline conditions, the solution is blue.
Chemical reactions are other than acid–base can also cause a color change to litmus paper. For instance, chlorine gas turns blue litmus paper white; the litmus dye is bleached because hypochlorite ions are present. This reaction is irreversible, so the litmus is not acting as an indicator in this situation. | 0 | Chromatography + Titration + pH indicators |
In any form of chromatography, the rate at which the solute moves down the column is a direct reflection of the percentage of time the solute spends in the mobile phase. To achieve separation in either elution or displacement chromatography, there must be appreciable differences in the affinity of the respective solutes for the stationary phase. Both methods rely on movement down the column to amplify the effect of small differences in distribution between the two phases. Distribution between the mobile and stationary phases is described by the binding isotherm, a plot of solute bound to (or partitioned into) the stationary phase as a function of concentration in the mobile phase. The isotherm is often linear, or approximately so, at low concentrations, but commonly curves (concave-downward) at higher concentrations as the stationary phase becomes saturated. | 0 | Chromatography + Titration + pH indicators |
Unit cell parameters (a,b,c,α,β,γ) can be computed from the final relaxed positions of the ions. In a NaCl calculation, the final position of the Na ion might be (0,0,0) in picometer Cartesian coordinates and the final position of the Cl ion might be (282,282,282). From this, we see that the lattice constant would be 584 pm. For non-orthorhombic systems, the determination of cell parameters might be more complicated, but many ab-initio numerical packages have utilities to make this calculation simpler.
Once the lattice cell parameters are known, patterns for single crystal or powder diffraction can be readily predicted via Bragg's Law. | 1 | Crystallography |
The majority of systems utilize two two-cylinder piston pumps, one for each buffer, combining the output of both in a mixing chamber. Some simpler systems use a single peristaltic pump which draws both buffers from separate reservoirs through a proportioning valve and mixing chamber. In either case the system allows the fraction of each buffer entering the column to be continuously varied. The flow rate can go from a few milliliters per minute in bench-top systems to liters per minute for industrial scale purifications. The wide flow range makes it suitable both for analytical and preparative chromatography. | 0 | Chromatography + Titration + pH indicators |
Eriochrome Black T is a complexometric indicator that is used in complexometric titrations, e.g. in the water hardness determination process. It is an azo dye. Eriochrome is a trademark of Huntsman Petrochemical, LLC.
In its deprotonated form, Eriochrome Black T is blue. It turns red when it forms a complex with calcium, magnesium, or other metal ions. | 0 | Chromatography + Titration + pH indicators |
Specifically, an SMB system has two or more identical columns, which are connected to the mobile phase pump, and each other, by a multi-port valve. The plumbing is configured in such a way that:
:a) all columns will be connected in series, forming a single continuous loop;
:b) typically, between each column there will be provisions for four process streams: incoming feed mixture, exiting purified fast component, exiting purified slow component, and incoming solvent or eluent;
and
:c) each process stream (two inlets and two outlets) will proceed in the same direction after a set time (the steptime). | 0 | Chromatography + Titration + pH indicators |
The leuco form of malachite green was first prepared by Hermann Fischer in 1877 by condensing benzaldehyde and dimethylaniline in the molecular ratio 1:2 in the presence of sulfuric acid. | 0 | Chromatography + Titration + pH indicators |
Medical use of HPLC typically use mass spectrometer (MS) as the detector, so the technique is called LC-MS or LC-MS/MS for tandem MS, where two types of MS are operated sequentially. When the HPLC instrument is connected to more than one detector, it is called a hyphenated LC system. Pharmaceutical applications are the major users of HPLC, LC-MS and LC-MS/MS. This includes drug development and pharmacology, which is the scientific study of the effects of drugs and chemicals on living organisms, personalized medicine, public health and diagnostics. While urine is the most common medium for analyzing drug concentrations, blood serum is the sample collected for most medical analyses with HPLC. One of the most important roles of LC-MS and LC-MS/MS in the clinical lab is the Newborn Screening (NBS) for metabolic disorders and follow-up diagnostics. The infants' samples come in the shape of dried blood spot (DBS), which is simple to prepare and transport, enabling safe and accessible diagnostics, both locally and globally.
Other methods of detection of molecules that are useful for clinical studies have been tested against HPLC, namely immunoassays. In one example of this, competitive protein binding assays (CPBA) and HPLC were compared for sensitivity in detection of vitamin D. Useful for diagnosing vitamin D deficiencies in children, it was found that sensitivity and specificity of this CPBA reached only 40% and 60%, respectively, of the capacity of HPLC. While an expensive tool, the accuracy of HPLC is nearly unparalleled. | 0 | Chromatography + Titration + pH indicators |
Another example is hematite on magnetite . The magnetite structure is based on close-packed oxygen anions stacked in an ABC-ABC sequence. In this packing the close-packed layers are parallel to (111) (a plane that symmetrically "cuts off" a corner of a cube). The hematite structure is based on close-packed oxygen anions stacked in an AB-AB sequence, which results in a crystal with hexagonal symmetry.
If the cations were small enough to fit into a truly close-packed structure of oxygen anions then the spacing between the nearest neighbour oxygen sites would be the same for both species. The radius of the oxygen ion, however, is only 1.36 Å and the Fe cations are big enough to cause some variations. The Fe radii vary from 0.49 Å to 0.92 Å, depending on the charge (2+ or 3+) and the coordination number (4 or 8). Nevertheless, the O spacings are similar for the two minerals hence hematite can readily grow on the (111) faces of magnetite, with hematite (001) parallel to magnetite (111). | 1 | Crystallography |
In geometric phase analysis, crystallographic quantities are not determined at one particular point of the input image. Instead, they are quantified across the whole image resulting in a two-dimensional map of given quantity. Quantities which can be mapped with geometric phase analysis include interplanar distances (d-spacing), strain tensor and displacement vector.
Since the calculations are performed in frequential domain, the input image of crystal lattice must be transformed into frequential representation using Fourier transform. From mathematical point of view, the frequential image is a complex matrix with the size equal to the original image. From crystallographic point of view, it can be seen as an artificial diffraction pattern or reciprocal image as it depicts reciprocal lattice. In this representation, the intensity peaks (or power peaks) correspond to the crystallographic planes depicted in the original image.
Due to the complex nature of the frequential image, it can be used to calculate amplitude and phase. Together with a vector of one crystallographic plane depicted in the image, the amplitude and phase can be used to generate a 2D map of d-spacing. If two vectors of non-parallel planes are known, the method can be used to generate maps of strain and displacement. | 1 | Crystallography |
The special cases of 2D (wallpaper groups) and 3D (space groups) are most heavily used in applications, and they can be treated together. | 1 | Crystallography |
For an infinite two-dimensional lattice, defined by its primitive vectors , its reciprocal lattice can be determined by generating its two reciprocal primitive vectors, through the following formulae,
where is an integer and
Here represents a 90 degree rotation matrix, i.e. a quarter turn. The anti-clockwise rotation and the clockwise rotation can both be used to determine the reciprocal lattice: If is the anti-clockwise rotation and is the clockwise rotation, for all vectors . Thus, using the permutation
we obtain
Notably, in a 3D space this 2D reciprocal lattice is an infinitely extended set of Bragg rods—described by Sung et al. | 1 | Crystallography |
More accurately, a single formula that describes the titration of a weak acid with a strong base from start to finish is given below:
where
" φ = fraction of completion of the titration (φ < 1 is before the equivalence point, φ = 1 is the equivalence point, and φ > 1 is after the equivalence point)
: = the concentrations of the acid and base respectively
: = the volumes of the acid and base respectively | 0 | Chromatography + Titration + pH indicators |
The chemical character of azo violet may be attributed to its azo group (-N=N-), six-membered rings, and hydroxyl side groups. Due to steric repulsions, azo violet is most stable in the trans-configuration, but isomerization of azo dyes by irradiation is not uncommon. The para-position tautomerization of azo violet provides mechanical insight into the behavior of the compound in an acidic environment, and thus its use as a basic pH indicator.
The predicted H-NMR of pure azo violet shows the hydroxyl protons as the most deshielded and acidic protons. The participation of these hydroxyl groups electron-donation to the conjugated π system likewise influences azo violets λ and pK value. | 0 | Chromatography + Titration + pH indicators |
After being scattered by the sample, the profile of the diffracted beam needs to be detected by a two-dimensionally resolving X-ray detector. The classical "detector" is X-ray sensitive film, with nuclear plates as a traditional alternative. The first step beyond these "offline" detectors were the so-called image plates, although limited in readout speed and spatial resolution. Since about the mid-1990s, CCD cameras have emerged as a practical alternative, offering many advantages such as fast online readout and the possibility to record entire image series in place. X-ray sensitive CCD cameras, especially those with spatial resolution in the micrometer range, are now well established as electronic detectors for topography. A promising further option for the future may be pixel detectors, although their limited spatial resolution may restrict their usefulness for topography.
General criteria for judging the practical usefulness of detectors for topography applications include spatial resolution, sensitivity, dynamic range ("color depth", in black-white mode), readout speed, weight (important for mounting on diffractometer arms), and price. | 1 | Crystallography |
The shape of a powder diffraction reflection is influenced by the characteristics of the beam, the experimental
arrangement, and the sample size and shape. In the case of monochromatic neutron sources the convolution
of the various effects has been found to result in a reflex almost exactly Gaussian in shape. If this
distribution is assumed then the contribution of a given reflection to the profile at position
is:
where is the full width at half peak height (full-width half-maximum), is the center of the reflex, and is the calculated intensity of the reflex (determined from the structure factor,
the Lorentz factor, and multiplicity of the reflection).
At very low diffraction angles the reflections may acquire an asymmetry due to the vertical divergence of the beam.
Rietveld used a semi-empirical correction factor, to account for this asymmetry:
where is the asymmetry factor and is , , or depending on the difference being positive, zero, or negative respectively.
At a given position more than one diffraction peak may contribute to the profile. The intensity is simply the sum of all reflections contributing at the point . | 1 | Crystallography |
Bromophenol is also used as a colour marker to monitor the process of agarose gel electrophoresis and polyacrylamide gel electrophoresis. Since bromophenol blue carries a slight negative charge at moderate pH, it will migrate in the same direction as DNA or protein in a gel; the rate at which it migrates varies according to gel density and buffer composition, but in a typical 1% agarose gel in a 1X TAE buffer or TBE buffer, bromophenol blue migrates at the same rate as a DNA fragment of about 300 base pairs, in 2% agarose as 150 bp. Xylene cyanol and orange G may also be used for this purpose. | 0 | Chromatography + Titration + pH indicators |
Conductometry is a measurement of electrolytic conductivity to monitor a progress of chemical reaction. Conductometry has notable application in analytical chemistry, where conductometric titration is a standard technique. In usual analytical chemistry practice, the term conductometry is used as a synonym of conductometric titration while the term conductimetry is used to describe non-titrative applications. Conductometry is often applied to determine the total conductance of a solution or to analyze the end point of titrations that include ions. | 0 | Chromatography + Titration + pH indicators |
The liquid chromatograph is complex and has sophisticated and delicate technology. In order to properly operate the system, there should be a minimum basis for understanding of how the device performs the data processing to avoid incorrect data and distorted results.
HPLC is distinguished from traditional ("low pressure") liquid chromatography because operational pressures are significantly higher (around 50–1400 bar), while ordinary liquid chromatography typically relies on the force of gravity to pass the mobile phase through the packed column. Due to the small sample amount separated in analytical HPLC, typical column dimensions are 2.1–4.6 mm diameter, and 30–250 mm length. Also HPLC columns are made with smaller adsorbent particles (1.5–50 μm in average particle size). This gives HPLC superior resolving power (the ability to distinguish between compounds) when separating mixtures, which makes it a popular chromatographic technique.
The schematic of an HPLC instrument typically includes solvents reservoirs, one or more pumps, a solvent-degasser, a sampler, a column, and a detector. The solvents are prepared in advance according to the needs of the separation, they pass through the degasser to remove dissolved gasses, mixed to become the mobile phase, then flow through the sampler, which brings the sample mixture into the mobile phase stream, which then carries it into the column. The pumps deliver the desired flow and composition of the mobile phase through the stationary phase inside the column, then directly into a flow-cell inside the detector. The detector generates a signal proportional to the amount of sample component emerging from the column, hence allowing for quantitative analysis of the sample components. The detector also marks the time of emergence, the retention time, which serves for initial identification of the component. More advanced detectors, provide also additional information, specific to the analytes characteristics, such as UV-VIS spectrum or mass spectrum, which can provide insight on its structural features. These detectors are in common use, such as UV/Vis, photodiode array (PDA) / diode array detector and mass spectrometry detector.
A digital microprocessor and user software control the HPLC instrument and provide data analysis. Some models of mechanical pumps in an HPLC instrument can mix multiple solvents together at a ratios changing in time, generating a composition gradient in the mobile phase. Most HPLC instruments also have a column oven that allows for adjusting the temperature at which the separation is performed.
The sample mixture to be separated and analyzed is introduced, in a discrete small volume (typically microliters), into the stream of mobile phase percolating through the column. The components of the sample move through the colum, each at a different velocity, which are a function of specific physical interactions with the adsorbent, the stationary phase. The velocity of each component depends on its chemical nature, on the nature of the stationary phase (inside the column) and on the composition of the mobile phase. The time at which a specific analyte elutes (emerges from the column) is called its retention time. The retention time, measured under particular conditions, is an identifying characteristic of a given analyte.
Many different types of columns are available, filled with adsorbents varying in particle size, porosity, and surface chemistry. The use of smaller particle size packing materials requires the use of higher operational pressure ("backpressure") and typically improves chromatographic resolution (the degree of peak separation between consecutive analytes emerging from the column). Sorbent particles may be ionic, hydrophobic or polar in nature.
The most common mode of liquid chromatography is reversed phase, whereby the mobile phases used, include any miscible combination of water or buffers with various organic solvents (the most common are acetonitrile and methanol). Some HPLC techniques use water-free mobile phases (see normal-phase chromatography below). The aqueous component of the mobile phase may contain acids (such as formic, phosphoric or trifluoroacetic acid) or salts to assist in the separation of the sample components. The composition of the mobile phase may be kept constant ("isocratic elution mode") or varied ("gradient elution mode") during the chromatographic analysis. Isocratic elution is typically effective in the separation of simple mixtures. Gradient elution is required for complex mixtures, with varying interactions with the stationary and mobile phases. This is the reason why in gradient elution the composition of the mobile phase is varied typically from low to high eluting strength. The eluting strength of the mobile phase is reflected by analyte retention times, as the high eluting strength speeds up the elution (resulting in shortening of retention times). For example, a typical gradient profile in reversed phase chromatography for might start at 5% acetonitrile (in water or aqueous buffer) and progress linearly to 95% acetonitrile over 5–25 minutes. Periods of constant mobile phase composition (plateau) may be also part of a gradient profile. For example, the mobile phase composition may be kept constant at 5% acetonitrile for 1–3 min, followed by a linear change up to 95% acetonitrile.
The chosen composition of the mobile phase depends on the intensity of interactions between various sample components ("analytes") and stationary phase (e.g., hydrophobic interactions in reversed-phase HPLC). Depending on their affinity for the stationary and mobile phases, analytes partition between the two during the separation process taking place in the column. This partitioning process is similar to that which occurs during a liquid–liquid extraction but is continuous, not step-wise.
In the example using a water/acetonitrile gradient, the more hydrophobic components will elute (come off the column) later, then, once the mobile phase gets richer in acetonitrile (i.e., in a mobile phase becomes higher eluting solution), their elution speeds up.
The choice of mobile phase components, additives (such as salts or acids) and gradient conditions depends on the nature of the column and sample components. Often a series of trial runs is performed with the sample in order to find the HPLC method which gives adequate separation. | 0 | Chromatography + Titration + pH indicators |
The defining property of a crystal is its inherent symmetry. Performing certain symmetry operations on the crystal lattice leaves it unchanged. All crystals have translational symmetry in three directions, but some have other symmetry elements as well. For example, rotating the crystal 180° about a certain axis may result in an atomic configuration that is identical to the original configuration; the crystal has twofold rotational symmetry about this axis. In addition to rotational symmetry, a crystal may have symmetry in the form of mirror planes, and also the so-called compound symmetries, which are a combination of translation and rotation or mirror symmetries. A full classification of a crystal is achieved when all inherent symmetries of the crystal are identified. | 1 | Crystallography |
Cryo crystallography enables X-ray data collection at cryogenic temperatures, typically 100 K.
*Crystals are transferred from the solution they have grown in (called mother liquor) to a solution with a cryo-protectant to prevent ice formation.
*Crystals are mounted in a glass fiber (as opposed to a capillary.)
*Crystals are cooled by dipping directly into liquid nitrogen and then placed in a cryo cold stream.
*Cryo cooled macromolecular crystals show reduced radiation damage by more than 70 times that at room temperature. | 1 | Crystallography |
The absorption of methyl orange on the UV/vis spectrum is between 350-550 nm, with its peak at 464 nm. This is in the green-purple visible light range and explains why methyl orange is, in fact, orange. | 0 | Chromatography + Titration + pH indicators |
For any 2-dimensional lattice, the unit cells are parallelograms, which in special cases may have orthogonal angles, equal lengths, or both. Four of the five two-dimensional Bravais lattices are represented using conventional primitive cells, as shown below.
The centered rectangular lattice also has a primitive cell in the shape of a rhombus, but in order to allow easy discrimination on the basis of symmetry, it is represented by a conventional cell which contains two lattice points. | 1 | Crystallography |
TLE uses continuous-wave lasers (typically with a wavelength of around 1000 nm) located outside the vacuum chamber to heat sources of material in order to generate a flux of vapor via evaporation or sublimation. Owing to the localized nature of the heat induced by the laser, a portion of the source may be transformed into a liquid state while the rest remains solid, such that the source acts as its own crucible. The strong absorption of light causes the laser-induced heat to be highly localized via the small diameter of the laser beam, which can also have the effect of confining the heat to the axis of the source. The resulting absorption corresponds to a typical photon penetration depth on the order of 2 nm due to the high absorption coefficients of α ~ 10 cm of many materials. Heat loss via conduction and radiation further localizes the high-temperature region close to the irradiated surface of the source. The localized character of the heating enables many materials to be grown by TLE from freestanding sources without a crucible. Owing to the direct transfer of energy from the laser to the source, TLE is more efficient than other evaporation techniques such as evaporation and molecular beam epitaxy, which typically rely on wire-based Joule heaters to reach high temperatures.
By heating the source, a flux of vapor is produced, the pressure of which frequently has an approximately exponential relation to temperature. The vapor is then deposited onto a substrate, which is heated via a laser. This laser-heated substrate allows the use of adsorption-controlled growth modes, similar to molecular beam epitaxy, ensuring precise control of the stoichiometry and temperature of the deposited film. This precise control is valuable for growing thin-film heterostructures of complex materials, such as high-T superconductors. By positioning all lasers outside of the evaporation chamber, contamination can be reduced compared to using in situ heaters, resulting in highly pure deposited films.
The deposition rate of the vapor impinging upon the substrate is controlled by adjusting the power of the incident source laser. The deposition rate frequently increases exponentially with source temperature, which in turn increases linearly with incident laser power.
The gas in the chamber can be incorporated in the deposition film. With the addition of an oxygen or ozone atmosphere, oxide films can readily be grown with TLE at pressures up to 10 hPa. | 1 | Crystallography |
Reflections, or mirror isometries, can be combined to produce any isometry. Thus isometries are an example of a reflection group. | 1 | Crystallography |
* F. Geiss (1987): Fundamentals of thin layer chromatography planar chromatography, Heidelberg, Hüthig,
* Justus G. Kirchner (1978): Thin-layer chromatography, 2nd edition, Wiley
* Joseph Sherma, Bernard Fried (1991): Handbook of Thin-Layer Chromatography (= Chromatographic Science. Bd. 55). Marcel Dekker, New York NY, .
* Elke Hahn-Deinstorp: Applied Thin-Layer Chromatography. Best Practice and Avoidance of Mistakes. Wiley-VCH, Weinheim u. a. 2000, | 0 | Chromatography + Titration + pH indicators |
Put simply, ion suppression describes the adverse effect on detector response due to reduced ionisation efficiency for analyte(s) of interest, resulting from the presence of species in the sample matrix which compete for ionisation, or inhibit efficient ionisation in other ways. Use of MS/MS as a means of detection may give the impression that there are no interfering species present, since no chromatographic impurities are detected. However, species which are not isobaric may still have an adverse effect on the sensitivity, accuracy and precision of the assay owing to suppression of the ionisation of the analyte of interest.
Although the precise chemical and physical factors involved in ion suppression are not fully understood, it has been proposed that basicity, high concentration, mass and more intuitively, co-elution with the analyte of interest are factors which should not be ignored.
The most common atmospheric pressure ionisation techniques used in LC-MS/MS are electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI). APCI is less prone to pronounced ion suppression than ESI, an inherent property of the respective ionisation mechanisms.
In APCI, the sole source of ion suppression can be attributed to the change of colligative properties in the solute during evaporization (King et al, J. Am. Soc. Mass Spectrom 2000, 11, 942-950).
ESI has a more complex ionisation mechanism, relying heavily on droplet charge excess and as such there are many more factors to consider when exploring the cause of ion suppression. It has been widely observed that for many analytes, at high concentrations, ESI exhibits a loss of detector response linearity, perhaps due to reduced charge excess caused by analyte saturation at the droplet surface, inhibiting subsequent ejection of gas phase ions from further inside the droplet. Thus competition for space and/or charge may be considered as a source of ion suppression in ESI. Both physical and chemical properties of analytes (e.g. basicity and surface activity) determine their inherent ionisation efficiency. Biological sample matrices naturally tend to contain many endogenous species with high basicity and surface activity, hence the total concentration of these species in the sample will quickly reach levels at which ion suppression should be expected.
Another explanation of ion suppression in ESI considers the physical properties of the droplet itself rather than the species present. High concentrations of interfering components give rise to an increased surface tension and viscosity, giving a reduction in desolvation (solvent evaporation), which is known to have a marked effect of ionisation efficiency.
The third proposed theory for ion suppression in ESI relates to the presence of non-volatile species which can either cause co-precipitation of analyte in the droplet (thus preventing ionisation) or prevent the contraction of droplet size to the critical radius required for the ion evaporation and/or charge residue mechanisms to form gas phase ions efficiently.
It is worthwhile to consider that the degree of ion suppression may be dependent on the concentration of the analyte being monitored. A higher analyte/matrix ratio can give a reduced effect of ion suppression. | 0 | Chromatography + Titration + pH indicators |
As an abstract graph, the Laves graph can be constructed as the maximal abelian covering graph of the complete graph . Being an abelian covering graph of means that the vertices of the Laves graph can be four-colored such that each vertex has neighbors of the other three colors and so that there are color-preserving symmetries taking any vertex to any other vertex with the same color. For the Laves graph in its geometric form with integer coordinates, these symmetries are translations that add even numbers to each coordinate (additionally, the offsets of all three coordinates must be congruent modulo four). When applying two such translations in succession, the net translation is irrespective of their order: they commute with each other, forming an abelian group. The translation vectors of this group form a three-dimensional lattice. Finally, being a maximal abelian covering graph means that there is no other covering graph of involving a higher-dimensional lattice. This construction justifies an alternative name of the Laves graph, the crystal.
A maximal abelian covering graph can be constructed from any finite graph ; applied to , the construction produces the (abstract) Laves graph, but does not give it the same geometric layout. Choose a spanning tree of , let be the number of edges that are not in the spanning tree (in this case, three non-tree edges), and choose a distinct unit vector in for each of these non-tree edges. Then, fix the set of vertices of the covering graph to be the ordered pairs where is a vertex of and is a vector in . For each such pair, and each edge adjacent to in , make an edge from to where is the zero vector if belongs to the spanning tree, and is otherwise the basis vector associated with , and where the plus or minus sign is chosen according to the direction the edge is traversed. The resulting graph is independent of the chosen spanning tree, and the same construction can also be interpreted more abstractly using homology.
Using the same construction, the hexagonal tiling of the plane is the maximal abelian covering graph of the three-edge dipole graph, and the diamond cubic is the maximal abelian covering graph of the four-edge dipole. The -dimensional integer lattice (as a graph with unit-length edges) is the maximal abelian covering graph of a graph with one vertex and self-loops. | 1 | Crystallography |
Prior to HPLC, scientists used benchtop column liquid chromatographic techniques. Liquid chromatographic systems were largely inefficient due to the flow rate of solvents being dependent on gravity. Separations took many hours, and sometimes days to complete. Gas chromatography (GC) at the time was more powerful than liquid chromatography (LC), however, it was obvious that gas phase separation and analysis of very polar high molecular weight biopolymers was impossible. GC was ineffective for many life science and health applications for biomolecules, because they are mostly non-volatile and thermally unstable at the high temperatures of GC. As a result, alternative methods were hypothesized which would soon result in the development of HPLC.
Following on the seminal work of Martin and Synge in 1941, it was predicted by Calvin Giddings, Josef Huber, and others in the 1960s that LC could be operated in the high-efficiency mode by reducing the packing-particle diameter substantially below the typical LC (and GC) level of 150 μm and using pressure to increase the mobile phase velocity. These predictions underwent extensive experimentation and refinement throughout the 60s into the 70s until these very days. Early developmental research began to improve LC particles, for example the historic Zipax, a superficially porous particle.
The 1970s brought about many developments in hardware and instrumentation. Researchers began using pumps and injectors to make a rudimentary design of an HPLC system. Gas amplifier pumps were ideal because they operated at constant pressure and did not require leak-free seals or check valves for steady flow and good quantitation. Hardware milestones were made at Dupont IPD (Industrial Polymers Division) such as a low-dwell-volume gradient device being utilized as well as replacing the septum injector with a loop injection valve.
While instrumentation developments were important, the history of HPLC is primarily about the history and evolution of particle technology. After the introduction of porous layer particles, there has been a steady trend to reduced particle size to improve efficiency. However, by decreasing particle size, new problems arose. The practical disadvantages stem from the excessive pressure drop needed to force mobile fluid through the column and the difficulty of preparing a uniform packing of extremely fine materials. Every time particle size is reduced significantly, another round of instrument development usually must occur to handle the pressure. | 0 | Chromatography + Titration + pH indicators |
Friedel's salt is a layered double hydroxide (LDH) of general formula:
or more explicitly for a positively-charged LDH mineral:
or by directly incorporating water molecules into the Ca,Al hydroxide layer:
where chloride and hydroxide anions occupy the interlayer to compensate the excess of positive charges.
In the cement chemist notation (CCN), considering that
and doubling all the stoichiometry, it could also be written in CCN as follows:
A simplified chemical composition with only Cl in the interlayer, and without OH, as:
can be also written in cement chemist notation as:
Friedels salt is formed in cements initially rich in tri-calcium aluminate (CA). Free-chloride ions directly bind with the AFm hydrates (CAH and its derivatives) to form Friedels salt. | 1 | Crystallography |
The history and evolution of reversed phase stationary phases in described in detail in an article by Majors, Dolan, Carr and Snyder.
In the 1970s, most liquid chromatography runs were performed using solid particles as the stationary phases, made of unmodified silica gel or alumina. This type of technique is now referred to as normal-phase chromatography. Since the stationary phase is hydrophilic in this technique, and the mobile phase is non-polar (consisting of organic solvents such as hexane and heptane), biomolecules with hydrophilic properties in the sample adsorb to the stationary phase strongly. Moreover, they were not dissolved easily in the mobile phase solvents. At the same time hydrophobic molecules experience less affinity to the polar stationary phase, and elute through it early with not enough retention. This was the reasons why during the 1970s the silica based particles were treated with hydrocarbons, immobilized or bonded on their surface, and the mobile phases were switched to aqueous and polar in nature, to accommodate biomedical substances.
The use of a hydrophobic stationary phase and polar mobile phases is essentially the reverse of normal phase chromatography, since the polarity of the mobile and stationary phases have been inverted – hence the term reversed-phase chromatography. As a result, hydrophobic molecules in the polar mobile phase tend to adsorb to the hydrophobic stationary phase, and hydrophilic molecules in the sample pass through the column and are eluted first. Hydrophobic molecules can be eluted from the column by decreasing the polarity of the mobile phase using an organic (non-polar) solvent, which reduces hydrophobic interactions. The more hydrophobic the molecule, the more strongly it will bind to the stationary phase, and the higher the concentration of organic solvent that will be required to elute the molecule.
Many of the mathematical parameters of the theory of chromatography and experimental considerations used in other chromatographic methods apply to RP-LC as well (for example, the selectivity factor, chromatographic resolution, plate count, etc. It can be used for the separation of a wide variety of molecules. It is typically used for separation of proteins, because the organic solvents used in normal-phase chromatography can denature many proteins.
Today, RP-LC is a frequently used analytical technique. There are huge variety of stationary phases available for use in RP-LC, allowing great flexibility in the development of the separation methods. | 0 | Chromatography + Titration + pH indicators |
A widely used coordinate system is the Cartesian coordinate system, which consists of orthonormal basis vectors. This means that,
and
However, when describing objects with crystalline or periodic structure a Cartesian coordinate system is often not the most useful as it does not often reflect the symmetry of the lattice in the simplest manner. | 1 | Crystallography |
GC–MS is increasingly used for detection of illegal narcotics, and may eventually supplant drug-sniffing dogs. A simple and selective GC–MS method for detecting marijuana usage was recently developed by the Robert Koch Institute in Germany. It involves identifying an acid metabolite of tetrahydrocannabinol (THC), the active ingredient in marijuana, in urine samples by employing derivatization in the sample preparation. GC–MS is also commonly used in forensic toxicology to find drugs and/or poisons in biological specimens of suspects, victims, or the deceased. In drug screening, GC–MS methods frequently utilize liquid-liquid extraction as a part of sample preparation, in which target compounds are extracted from blood plasma. | 0 | Chromatography + Titration + pH indicators |
In chromatography, the retardation factor, R, is the fraction of the sample in the mobile phase at equilibrium, defined as: | 0 | Chromatography + Titration + pH indicators |
The Zener ratio is a dimensionless number that is used to quantify the anisotropy for cubic crystals. It is sometimes referred as anisotropy ratio and is named after Clarence Zener. Conceptually, it quantifies how far a material is from being isotropic (where the value of 1 means an isotropic material).
Its mathematical definition is
where refers to Elastic constants in Voigt notation. | 1 | Crystallography |
Chromatography is a common technique used in the field of Forensic Science. Chromatography is a method of separating the components of a mixture from a mobile phase. Chromatography is an essential tool used in forensic science, helping analysts identify and compare trace amounts of samples including ignitable liquids, drugs, and biological samples. Many laboratories utilize gas chromatography/mass spectrometry (GC/MS) to examine these kinds of samples; this analysis provides rapid and reliant data to identify samples in question. | 0 | Chromatography + Titration + pH indicators |
In a mirror furnace, material is heated by the lamps whose radiation is focused by mirrors. They are widely used for growing single crystals for scientific purposes, using the "floating zone" method. | 1 | Crystallography |
There are just 230 different ways of arranging objects in regular three-dimensional arrays. In molecular crystallography, these arrangements are called space groups. However, only 65 of these arrangements are accessible to chiral objects or chiral molecules. The remaining 165 space groups contain either a center of symmetry or a mirror plane and are thus not accessible to natural globular proteins, which are chiral molecules. Wukowitz and Yeates developed a mathematical theory to explain the preference of globular proteins to crystallize in certain space groups. They suggested the preferred space group was determined by the number of degrees of freedom (D) or dimensionality as a measure of the ease with which a given symmetry can be formed. They analyzed the number of degrees of freedom for both chiral and achiral space groups where it was found that the space group P1(bar) with D=8 is theoretically the most dominant space group. Since the achiral space group had a higher degree of freedom compared to the chiral space groups, they predicted that racemic mixtures of protein enantiomers would crystallize more readily compared to the natural L-proteins alone by forming achiral {L-protein plus D-protein} pairs. While space group P1(bar) is most preferred, P21/c and C2/c are also highly preferred, whereas the other achiral space groups are expected to appear less frequently. Hence, P1(bar), P21/c, and C2/c are considered common centrosymmetric space groups in racemic mixtures. | 1 | Crystallography |
Between 1936 and 1940, Japanese chemist and lichenologist Yasuhiko Asahina published a series of papers in the Journal of Japanese Botany detailing the microcrystallization technique. This simple and rapid method allowed for the identification of major metabolites in hundreds of lichen species, contributing significantly to taxonomic research. The technique was introduced to western lichenologists in a 1943 publication by Alexander Evans, and was used regularly until more advanced techniques such as thin-layer chromatography and high-performance liquid chromatography were introduced and integrated into laboratories. Decades of research on the secondary metabolites of lichens culminated in the publication of Identification of Lichen Substances, a 1996 work by Siegfried Huneck and Isao Yoshimura, that summarized analytical data for hundreds of lichen molecules, including images of microcrystals. Ultimately, the microcrystallization method had limitations, as it was unable to detect minor components or analyze complex mixtures of lichen substances. Despite these drawbacks, microcrystallization played a crucial role in the study of correlations between lichen chemistry, morphology, and geographic distribution. | 1 | Crystallography |
The dopped stone is ground at precise angles and indexes on cutting laps of progressively finer grit, and then the process is repeated a final time to polish each facet. Accurate repetition of angles in the cutting and polishing process is aided by the angle readout and index gear. The physical process of polishing is a subject of debate. One commonly accepted theory is that the fine abrasive particles of a polishing compound produce abrasions smaller than the wavelengths of light, thus making the minute scratches invisible. Since gemstones have two sides (the crown and pavilion), a device often called a "transfer jig" is used to flip the stone so that each side may be cut and polished. | 1 | Crystallography |
A relatively new topography-related technique (first published in 1996) is the so-called reticulography. Based on white-beam topography, the new aspect consists in placing a fine-scaled metallic grid ("reticule") between sample and detector. The metallic grid lines are highly absorbing, producing dark lines in the recorded image. While for flat, homgeneous sample the image of the grid is rectilinear, just as the grid itself, strongly deformed grid images may occur in the case of tilted or strained sample. The deformation results from Bragg angle changes (and thus different directions of propagation of the diffracted beams) due to lattice parameter differences (or tilted crystallites) in the
sample. The grid serves to split the diffracted beam into an array of microbeams, and to backtrace the propagation of each individual microbeam onto the sample surface. By recording reticulographic images at several sample-to-detector distances, and appropriate data processing, local distributions of misorientation across the sample surface can be derived. | 1 | Crystallography |
A circular filter paper is taken and the sample is deposited at the center of the paper. After drying the spot, the filter paper is tied horizontally on a Petri dish containing solvent, so that the wick of the paper is dipped in the solvent. The solvent rises through the wick and the components are separated into concentric rings. | 0 | Chromatography + Titration + pH indicators |
The contact graph of an arbitrary finite packing of unit balls is the graph whose vertices correspond to the packing elements and whose two vertices are connected by an edge if the corresponding two packing elements touch each other. The cardinality of the edge set of the contact graph gives the number of touching pairs, the number of 3-cycles in the contact graph gives the number of touching triplets, and the number of tetrahedrons in the contact graph gives the number of touching quadruples (in general for a contact graph associated with a sphere packing in n dimensions that the cardinality of the set of n-simplices in the contact graph gives the number of touching (n + 1)-tuples in the sphere packing). In the case of 3-dimensional Euclidean space, non-trivial upper bounds on the number of touching pairs, triplets, and quadruples were proved by Karoly Bezdek and Samuel Reid at the University of Calgary.
The problem of finding the arrangement of n identical spheres that maximizes the number of contact points between the spheres is known as the "sticky-sphere problem". The maximum is known for n ≤ 11, and only conjectural values are known for larger n. | 1 | Crystallography |
Different methods to determine the endpoint include:
*Indicator: A substance that changes color in response to a chemical change. An acid–base indicator (e.g., phenolphthalein) changes color depending on the pH. Redox indicators are also used. A drop of indicator solution is added to the titration at the beginning; the endpoint has been reached when the color changes.
*Potentiometer: An instrument that measures the electrode potential of the solution. These are used for redox titrations; the potential of the working electrode will suddenly change as the endpoint is reached.
*pH meter: A potentiometer with an electrode whose potential depends on the amount of H ion present in the solution. (This is an example of an ion-selective electrode.) The pH of the solution is measured throughout the titration, more accurately than with an indicator; at the endpoint there will be a sudden change in the measured pH.
*Conductivity: A measurement of ions in a solution. Ion concentration can change significantly in a titration, which changes the conductivity. (For instance, during an acid–base titration, the H and OH ions react to form neutral HO.) As total conductance depends on all ions present in the solution and not all ions contribute equally (due to mobility and ionic strength), predicting the change in conductivity is more difficult than measuring it.
*Color change: In some reactions, the solution changes color without any added indicator. This is often seen in redox titrations when the different oxidation states of the product and reactant produce different colors.
*Precipitation: If a reaction produces a solid, a precipitate will form during the titration. A classic example is the reaction between Ag and Cl to form the insoluble salt AgCl. Cloudy precipitates usually make it difficult to determine the endpoint precisely. To compensate, precipitation titrations often have to be done as "back" titrations (see below).
*Isothermal titration calorimeter: An instrument that measures the heat produced or consumed by the reaction to determine the endpoint. Used in biochemical titrations, such as the determination of how substrates bind to enzymes.
*Thermometric titrimetry: Differentiated from calorimetric titrimetry because the heat of the reaction (as indicated by temperature rise or fall) is not used to determine the amount of analyte in the sample solution. Instead, the endpoint is determined by the rate of temperature change.
*Spectroscopy: Used to measure the absorption of light by the solution during titration if the spectrum of the reactant, titrant or product is known. The concentration of the material can be determined by Beer's Law.
*Amperometry: Measures the current produced by the titration reaction as a result of the oxidation or reduction of the analyte. The endpoint is detected as a change in the current. This method is most useful when the excess titrant can be reduced, as in the titration of halides with Ag. | 0 | Chromatography + Titration + pH indicators |
*[http://www.isallaboutmath.com/proof.aspx Proof about Stereographic Projection taking circles in the sphere to circles in the plane] | 1 | Crystallography |
Sulfites and hydrogensulfites reduce iodine readily in acidic medium to iodide. Thus when a diluted but excess amount of standard iodine solution is added to known volume of sample, the sulfurous acid and sulfites present reduces iodine quantitatively:
(This application is used for iodimetry titration because here Iodine is directly used) | 0 | Chromatography + Titration + pH indicators |
Alizarine Yellow R is a yellow colored azo dye made by the diazo coupling reaction. It is usually commercially available as a sodium salt. In its pure form, it is a rust-colored solid. It is mainly used as a pH indicator. | 0 | Chromatography + Titration + pH indicators |
An epitaxial layer can be doped during deposition by adding impurities to the source gas, such as arsine, phosphine, or diborane. Dopants in the source gas, liberated by evaporation or wet etching of the surface, may also diffuse into the epitaxial layer and cause autodoping. The concentration of impurity in the gas phase determines its concentration in the deposited film. Doping can also be achieved by a site-competition technique, where the growth precursor ratios are tuned to enhance the incorporation of vacancies, specific dopant species or vacant-dopant clusters into the lattice. Additionally, the high temperatures at which epitaxy is performed may allow dopants to diffuse into the growing layer from other layers in the wafer (out-diffusion). | 1 | Crystallography |
There are a number of common formats for performing gel filtration for smaller (less than 4mL) volumes:
* Chromatography columns
* Gravity-flow columns
* Chromatography cartridges
* Centrifuge columns
* Centrifuge plates
Gravity-flow, or drip, columns use head-pressure from a buffer-chase to push the sample through the gel filtration matrix. Sample is loaded into the top of an upright column and allowed to flow into the resin bed. The sample is then chased through the column by adding additional buffer or water to the top of the column. During this process, small fractions are typically collected and each is tested for the macromolecules of interest. In some cases, several fractions might contain the protein and may have to be pooled to improve yield. In order to eliminate the time and monitoring assorted with drip columns, fractions often equal to the full exclusion volume of the column are collected regardless of sample volume resulting in significant dilution of sample.
Sealed chromatography cartridges or columns work similarly except the sample and buffer is pumped into and through the resin by an external device such as a liquid chromatographic (LC) system, also requiring collection and monitoring of several fractions. Even though this method is often semi-automated, using chromatography cartridges is typically limited to processing one sample at a time and some sample dilution from the chase buffer is still likely to occur.
To eliminate sample dilution and the collecting and monitoring of fractions, centrifuge column or plate -based gel filtration, also referred to as spin desalting, methods are commonly used. Spin desalting is unique in that a centrifuge is used to first clear the void volume of liquid in the resin, followed by sample addition and centrifugation. After centrifugation, the macromolecules in the sample have moved through the column in approximately the same initial volume, but the small molecules have been forced into the pores of the resin and replaced by the buffer that was used to pre-equilibrate the gel-filtration matrix. Spin columns and plates eliminate the need to wait for samples to emerge by gravity flow and require no chromatography system, allowing for multiple-sample processing simultaneously. | 0 | Chromatography + Titration + pH indicators |
:Diffraction patterns collected through PED often agree well-enough with the kinematical pattern to serve as input data for direct methods calculations. A three-dimensional set of intensities mapped over the reciprocal lattice can be generated by collecting diffraction patterns over multiple zone axes. Applying direct methods to this data set will then yield probable crystal structures. Coupling direct methods results with simulations (e.g. multislice) and iteratively refining the solution can lead to the ab initio determination of the crystal structure.
:The PED technique has been used to determine the crystal structure of many classes of materials. Initial investigations during the emergence of the technique focused on complex oxides and nano-precipitates in Aluminum alloys that could not be resolved using x-ray diffraction. Since becoming a more widespread crystallographic technique, many more complex metal oxide structures have been solved.
:Zeolites are a technologically valuable class of materials that have historically been difficult to solve using x-ray diffraction due to the large unit cells that typically occur. PED has been demonstrated to be a viable alternative to solving many of these structures, including the ZSM-10, MCM-68, and many of the ITQ-n class of zeolite structures.
:PED also enables the use of electron diffraction to investigate beam-sensitive organic materials. Because PED can reproduce symmetric zone axis diffraction patterns even when the zone axis is not perfectly aligned, it enables information to be extracted from sensitive samples without risking overexposure during a time-intensive orientation of the sample. | 1 | Crystallography |
Modification had also been extended past hydrophobic and hydrophilic attachments, charged compounds have also been introduced to TRPs. Kobayashi et al. had previously performed successful modifications to separate bioactive ionic compounds, and continued on that success to improve separation efficiency of bioactive compounds. Common methods of separating angiotensin peptides had involved reverse-phased high-performance liquid chromatography (RP-HPLC) and cation-exchange chromatography. RP-HPLC requires the use of organic solvents, which is not favored and current trends are moving away from that. Hydrophobic interaction chromatography requires high concentration salt elutions and eluent cleaning to remove the salt. To address the shortcomings of the previous methods, Kobayashi’s group grafted acrylic acid (anionic acrylate under neutral conditions) and tert-butylacrylamide (hydrophobic) monomers onto PNIPAAm, resulting in PNIPAAm-co-AAc-co-tBAAm (IAtB) onto silica beads as a stationary phase medium. The reason for incorporating both ionic and hydrophobic compounds is multifaceted. The ionic compound improves interactivity with the ionic species, but raises the LCST significantly. The hydrophobic addition counteracts against the raise in LCST and lowers it to a more standard value, but also interacts with the hydrophobic surfaces of biological compounds. This resulted in successful and resolved elution of angiotensin peptides. Additionally, they were able to tune the retention factor for the analytes through isocratic temperature gradient elution. Ideal elutions occurred at 35 °C, but decreasing the temperature to 10 °C or raising it to 50 °C caused faster elutions either way. This is a strong indication that electrostatic and hydrophobic interactions can be similarly affected by changes in temperature. The major advantages from applying these success of this study include stationary phase versatility and maintaining bioactivity of the analytes.
Ayano et al. modified PNIPAAm with cationic N,N-dimethylaminopropylacrylamide (DMAPAAm) and hydrophobic BMA and grafted it onto silica beads to form IDB. They used pH changes to adjust the LCST. The effect of pH on the LCST is as follows, from a plateau value between pH 4.5 and pH 6.0, the LCST decreased up to pH 9 and below pH 4.5. This can be interpreted as requiring slightly basic or moderately acidic conditions, as the 4.5–6.0 pH region holds a maximum value of the LCST, an unfavorable condition. They used these properties to separate several non-steroidal anti-inflammatory drugs (NSAIDs). The analysis of acidic drugs (salicylic acid: BA; SA; MS; and As) was performed below pH 4.5. MS is hydrophobic only its retention time was affected by an increase in temperature on the column without a terminally modified anion-exchanger (IB column). However, with an anion-exchanger present, dissociated acidic drugs were retained longer at temperatures below LCST, and shorter at temperatures above LCST. When the IBD column compared to recently established PNIPAAm columns, electrostatic forces show remarkably higher retention ability of charged compounds than its hydrophilic predecessor. A single stationary phase can accomplish pharmaceutical separations based on hydrophobic interactions, hydrophilic interactions, and electrostatic interactions merely by adjusting the temperature (while adjusting pH to tweak the LCST). | 0 | Chromatography + Titration + pH indicators |
Some forensic techniques, believed to be scientifically sound at the time they were used, have turned out later to have much less scientific merit or none. Some such techniques include:
* Comparative bullet-lead analysis was used by the FBI for over four decades, starting with the John F. Kennedy assassination in 1963. The theory was that each batch of ammunition possessed a chemical makeup so distinct that a bullet could be traced back to a particular batch or even a specific box. Internal studies and an outside study by the National Academy of Sciences found that the technique was unreliable due to improper interpretation, and the FBI abandoned the test in 2005.
* Forensic dentistry has come under fire: in at least three cases bite-mark evidence has been used to convict people of murder who were later freed by DNA evidence. A 1999 study by a member of the American Board of Forensic Odontology found a 63 percent rate of false identifications and is commonly referenced within online news stories and conspiracy websites. The study was based on an informal workshop during an ABFO meeting, which many members did not consider a valid scientific setting. The theory is that each person has a unique and distinctive set of teeth, which leave a pattern after biting someone. They analyze the dental characteristics such as size, shape, and arch form.
* In 2009, scientists were able to show that it is possible to fabricate DNA evidence, thus "undermining the credibility of what has been considered the gold standard of proof in criminal cases".
* Police Access to Genetic Genealogy Databases: There are privacy concerns with the police being able to access personal genetic data that is on genealogy services. Individuals can become criminal informants to their own families or to themselves simply by participating in genetic genealogy databases. The Combined DNA Index System (CODIS) is a database that the FBI uses to hold genetic profiles of all known felons, misdemeanants, and arrestees. Some people argue that individuals who are using genealogy databases should have an expectation of privacy in their data that is or may be violated by genetic searches by law enforcement. These different services have warning signs about potential third parties using their information, but most individuals do not read the agreement thoroughly. According to a study by Christi Guerrini, Jill Robinson, Devan Petersen, and Amy McGuire, they found that the majority of the people who took the survey support police searches of genetic websites that identify genetic relatives. People who responded to the survey are more supportive of police activities using genetic genealogy when it is for the purpose of identifying offenders of violent crimes, suspects of crimes against children or missing people. The data from the surveys that were given show that individuals are not concerned about police searches using personal genetic data if it is justified. It was found in this study that offenders are disproportionally low-income and black and the average person of genetic testing is wealthy and white. The results from the study had different results. In 2016, there was a survey called the National Crime Victimization Survey (NCVS) that was provided by the US Bureau of Justice Statistics. In that survey, it was found that 1.3% of people aged 12 or older were victims of violent crimes, and 8.85 of households were victims of property crimes. There were some issues with this survey though. The NCVS produces only the annual estimates of victimization. The survey that Christi Guerrini, Jill Robinson, Devan Petersen, and Amy McGuire produced asked the participants about the incidents of victimization over one's lifetime. Their survey also did not restrict other family members to one household. Around 25% of people who responded to the survey said that they have had family members that have been employed by law enforcement which includes security guards and bailiffs. Throughout these surveys, it has been found that there is public support for law enforcement to access genetic genealogy databases. | 0 | Chromatography + Titration + pH indicators |
Numerous niche applications exploit the intense color of MG. It is used as a biological stain for microscopic analysis of cell biology and tissue samples. In the Gimenez staining method, basic fuchsin stains bacteria red or magenta, and malachite green is used as a blue-green counterstain. Malachite green is also used in endospore staining, since it can directly stain endospores within bacterial cells; here a safranin counterstain is often used. Malachite green is a part of Alexander's pollen stain. Malachite green can also be used as a saturable absorber in dye lasers, or as a pH indicator between pH 0.2–1.8. However, this use is relatively rare. Leuco-malachite green (LMG) is used as a detection method for latent blood in forensic science. Hemoglobin catalyzes the reaction between LMG and hydrogen peroxide, converting the colorless LMG into malachite green. Therefore, the appearance of a green color indicates the presence of blood.
A set of malachite green derivatives is also a key component in a fluorescence microscopy tool called the fluorogen activating protein/fluorogen system. Malachite green is in a class of molecules called fluorophores. When malachite greens rotational freedom is restricted, it transforms from a non fluorescent molecule to a highly fluorescent molecule. In the fluorogen activating protein tool, established by a group at Carnegie Mellon University, Malachite green binds a specific fluorogen activating protein to become highly fluorescent. Expression of the fluorogen activating protein as fusions of targeting domains can impart subcellular localization. Its use is similar to that of GFP but has the added benefit of having a dark state' before the malachite green fluorophore is added. This is especially useful for FRET studies. | 0 | Chromatography + Titration + pH indicators |
Crystal violet is one of the components of methyl violet, a dye first synthesized by Charles Lauth in 1861. From 1866, methyl violet was manufactured by the Saint-Denis-based firm of Poirrier et Chappat and marketed under the name "Violet de Paris". It was a mixture of the tetra-, penta- and hexamethylated pararosanilines.
Crystal violet itself was first synthesized in 1883 by Alfred Kern (1850–1893) working in Basel at the firm of Bindschedler and Busch. To optimize the difficult synthesis which used the highly toxic phosgene, Kern entered into a collaboration with the German chemist Heinrich Caro at BASF. Kern also found that by starting with diethylaniline rather than dimethylaniline, he could synthesize the closely related violet dye now known as C.I. 42600 or C.I. Basic violet 4. | 0 | Chromatography + Titration + pH indicators |
White-beam topography uses the full bandwidth of X-ray wavelengths in the incoming beam, without any wavelength filtering (no monochromator). The technique is particularly useful in combination with synchrotron radiation sources, due to their wide and continuous wavelength spectrum. In contrast to the monochromatic case, in which accurate sample adjustment is often necessary in order to reach diffraction conditions, the Bragg equation is always and automatically fulfilled in the case of a white X-ray beam: Whatever the angle at which the beam hits a specific lattice plane, there is always one wavelength in the incident spectrum for which the Bragg angle is fulfilled just at this precise angle (on condition that the spectrum is wide enough). White-beam topography is therefore a very simple and fast technique. Disadvantages include the high X-ray dose, possibly leading to radiation damage to the sample, and the necessity to carefully shield the experiment.
White-beam topography produces a pattern of several diffraction spots, each spot being related to one specific lattice plane in the crystal. This pattern, typically recorded on X-ray film, corresponds to a Laue pattern and shows the symmetry of the crystal lattice. The fine structure of each single spot (topograph) is related to defects and distortions in the sample. The distance between spots, and the details of contrast within one single spot, depend on the distance between sample and film; this distance is therefore an important degree of freedom for white-beam topography experiments.
Deformation of the crystal will cause variation in the size of the diffraction spot. For a cylindrically bent crystal the Bragg planes in the crystal lattice will lie on Archimedean spirals (with the exception of those orientated tangentially and radially to the curvature of the bend, which are respectively cylindrical and planar), and the degree of curvature can be determined in a predictable way from the length of the spots and the geometry of the set-up.
White-beam topographs are useful for fast and comprehensive visualization of crystal defect and distortions. They are, however, rather difficult to analyze in any quantitative way, and even a qualitative interpretation often requires considerable experience and time. | 1 | Crystallography |
A rule-of-thumb is that any molecule that will dissolve in methanol or a less polar solvent is compatible with SFC, including non-volatile polar solutes. CO has polarity similar to n-heptane at its critical point. The solvent's elution strength can be increased just by increasing density or alternatively, using a polar co-solvent. In practice, when the fraction of the co-solvent is high, the mobile phase might not be truly at supercritical fluid state, but this terminology is used regardless, and the chromatograms show better elution and higher efficiency nevertheless. | 0 | Chromatography + Titration + pH indicators |
Perovskites may be structured in layers, with the structure separated by thin sheets of intrusive material. Different forms of intrusions, based on the chemical makeup of the intrusion, are defined as:
* Aurivillius phase: the intruding layer is composed of a [] ion, occurring every n layers, leading to an overall chemical formula of []-. Their oxide ion-conducting properties were first discovered in the 1970s by Takahashi et al., and they have been used for this purpose ever since.
* Dion−Jacobson phase: the intruding layer is composed of an alkali metal (M) every n layers, giving the overall formula as
* Ruddlesden-Popper phase: the simplest of the phases, the intruding layer occurs between every one (n = 1) or multiple (n > 1) layers of the lattice. Ruddlesden−Popper phases have a similar relationship to perovskites in terms of atomic radii of elements with A typically being large (such as La or Sr) with the B ion being much smaller typically a transition metal (such as Mn, Co or Ni). Recently, hybrid organic-inorganic layered perovskites have been developed, where the structure is constituted of one or more layers of MX-octahedra, where M is a +2 metal (such as Pb or Sn) and X and halide ion (such as ), separated by layers of organic cations (such as butylammonium- or phenylethylammonium-cation). | 1 | Crystallography |
To image time-dependent, periodically fluctuating phenomena, topography can be combined with stroboscopic exposure techniques. In this way, one selected phase of a sinusoidally varying movement is selectively images as a "snapshot". First applications were in the field of surface acoustic waves on semiconductor surfaces.
Literature: | 1 | Crystallography |
These groups may contain only two-fold axes, mirror planes, and/or an inversion center. These are the crystallographic point groups 1 and (triclinic crystal system), 2, m, and (monoclinic), and 222, , and mm2 (orthorhombic). (The short form of is mmm.) If the symbol contains three positions, then they denote symmetry elements in the x, y, z direction, respectively. | 1 | Crystallography |
Chromatofocusing is a protein-separation technique that allows resolution of single proteins and other ampholytes from a complex mixture according to differences in their isoelectric point. Chromatofocusing uses ion exchange resins and is typically performed on fast protein liquid chromatography (FPLC) or similar equipment capable of producing continuous buffer gradients, though this is not a requirement.
In contrast to typical ion exchange chromatography, where bound molecules are eluted from the resin by increasing the ionic strength of the buffer environment, chromatofocusing elutes bound species by altering the pH of the buffer. This changes the net surface charge of bound molecules, altering their avidity for the resin. As the changing pH of the buffer system traverses the pI of a given molecule, that molecule will elute from the resin as it will no longer possess a net surface charge (a requisite for molecular binding to ion exchange resins).
Chromatofocusing is a powerful purification technique with respect to proteins as it can resolve very similar species differing by less than 0.05 pH units that may not separate well, or at all, using traditional ion exchange strategies.
A major drawback to this technique is that some proteins will aggregate when they are present at relatively high concentrations and carry no net surface charge. This can cause blockage of the resin, which is highly problematic when using sealed columns of ion exchange resin on FPLC equipment, resulting in pressure buildup and possible equipment failure. Apparent aggregation issues can sometimes be overcome by limiting the sample concentration and use of buffer additives that deter aggregate formation. | 0 | Chromatography + Titration + pH indicators |
Ballistics is "the science of the motion of projectiles in flight". In forensic science, analysts examine the patterns left on bullets and cartridge casings after being ejected from a weapon. When fired, a bullet is left with indentations and markings that are unique to the barrel and firing pin of the firearm that ejected the bullet. This examination can help scientists identify possible makes and models of weapons connected to a crime.
Henry Goddard at Scotland Yard pioneered the use of bullet comparison in 1835. He noticed a flaw in the bullet that killed the victim and was able to trace this back to the mold that was used in the manufacturing process. | 0 | Chromatography + Titration + pH indicators |
Researchers in structural geology are concerned with the orientations of planes and lines for a number of reasons. The foliation of a rock is a planar feature that often contains a linear feature called lineation. Similarly, a fault plane is a planar feature that may contain linear features such as slickensides.
These orientations of lines and planes at various scales can be plotted using the methods of the Visualization of lines and planes section above. As in crystallography, planes are typically plotted by their poles. Unlike crystallography, the southern hemisphere is used instead of the northern one (because the geological features in question lie below the Earth's surface). In this context the stereographic projection is often referred to as the equal-angle lower-hemisphere projection. The equal-area lower-hemisphere projection defined by the Lambert azimuthal equal-area projection is also used, especially when the plot is to be subjected to subsequent statistical analysis such as density contouring. | 1 | Crystallography |
Diamonds cubic structure is in the Fdm space group (space group 227), which follows the face-centered cubic Bravais lattice. The lattice describes the repeat pattern; for diamond cubic crystals this lattice is "decorated" with a motif of two tetrahedrally bonded atoms in each primitive cell, separated by of the width of the unit cell in each dimension. The diamond lattice can be viewed as a pair of intersecting face-centered cubic lattices, with each separated by of the width of the unit cell in each dimension. Many compound semiconductors such as gallium arsenide, β-silicon carbide, and indium antimonide adopt the analogous zincblende structure, where each atom has nearest neighbors of an unlike element. Zincblendes space group is F3m, but many of its structural properties are quite similar to the diamond structure.
The atomic packing factor of the diamond cubic structure (the proportion of space that would be filled by spheres that are centered on the vertices of the structure and are as large as possible without overlapping) is significantly smaller (indicating a less dense structure) than the packing factors for the face-centered and body-centered cubic lattices. Zincblende structures have higher packing factors than 0.34 depending on the relative sizes of their two component atoms.
The first-, second-, third-, fourth-, and fifth-nearest-neighbor distances in units of the cubic lattice constant are respectively. | 1 | Crystallography |
As an acid–base indicator, its useful range lies between pH 3.0 and 4.6. It changes from yellow at pH 3.0 to blue at pH 4.6; this reaction is reversible. Bromophenol blue is structurally related to phenolphthalein (a popular indicator). | 0 | Chromatography + Titration + pH indicators |
SMB provides lower production cost by requiring less column volume, less chromatographic separation media ("packing" or "stationary phase"), using less solvent and less energy, and requiring far less labor.
At industrial scale an SMB chromatographic separator is operated continuously, requiring less resin and less solvent than batch chromatography. The continuous operation facilitates operation control and integration into production plants. | 0 | Chromatography + Titration + pH indicators |
A type of ion exchange chromatography, membrane exchange is a relatively new method of purification designed to overcome limitations of using columns packed with beads. Membrane Chromatographic devices are cheap to mass-produce and disposable unlike other chromatography devices that require maintenance and time to revalidate. There are three types of membrane absorbers that are typically used when separating substances. The three types are flat sheet, hollow fibre, and radial flow. The most common absorber and best suited for membrane chromatography is multiple flat sheets because it has more absorbent volume. It can be used to overcome mass transfer limitations and pressure drop, making it especially advantageous for isolating and purifying viruses, plasmid DNA, and other large macromolecules. The column is packed with microporous membranes with internal pores which contain adsorptive moieties that can bind the target protein. Adsorptive membranes are available in a variety of geometries and chemistry which allows them to be used for purification and also fractionation, concentration, and clarification in an efficiency that is 10 fold that of using beads. Membranes can be prepared through isolation of the membrane itself, where membranes are cut into squares and immobilized. A more recent method involved the use of live cells that are attached to a support membrane and are used for identification and clarification of signaling molecules. | 0 | Chromatography + Titration + pH indicators |
Matrix-assisted inlet ionization (MAII) has shown that the laser is not necessary for the ionization process. Ions are formed when matrix-analyte is introduced to the vacuum of a mass spectrometer through an inlet aperture. LSI is a subset of MAII and is now called laserspray inlet ionization (LSII). Laser spray inlet ionization and matrix-assisted inlet ionization can be coupled to a fourier transform ion cyclotron resonance (FT-ICR) mass analyzer to improve detection of peptides and proteins. | 0 | Chromatography + Titration + pH indicators |
In physics, a Bragg plane is a plane in reciprocal space which bisects a reciprocal lattice vector, , at right angles. The Bragg plane is defined as part of the Von Laue condition for diffraction peaks in x-ray diffraction crystallography.
Considering the adjacent diagram, the arriving x-ray plane wave is defined by:
Where is the incident wave vector given by:
where is the wavelength of the incident photon. While the Bragg formulation assumes a unique choice of direct lattice planes and specular reflection of the incident X-rays, the Von Laue formula only assumes monochromatic light and that each scattering center acts as a source of secondary wavelets as described by the Huygens principle. Each scattered wave contributes to a new plane wave given by:
The condition for constructive interference in the direction is that the path difference between the photons is an integer multiple (m) of their wavelength. We know then that for constructive interference we have:
where . Multiplying the above by we formulate the condition in terms of the wave vectors, and :
Now consider that a crystal is an array of scattering centres, each at a point in the Bravais lattice. We can set one of the scattering centres as the origin of an array. Since the lattice points are displaced by the Bravais lattice vectors, , scattered waves interfere constructively when the above condition holds simultaneously for all values of which are Bravais lattice vectors, the condition then becomes:
An equivalent statement (see mathematical description of the reciprocal lattice) is to say that:
By comparing this equation with the definition of a reciprocal lattice vector, we see that constructive interference occurs if is a vector of the reciprocal lattice. We notice that and have the same magnitude, we can restate the Von Laue formulation as requiring that the tip of incident wave vector, , must lie in the plane that is a perpendicular bisector of the reciprocal lattice vector, . This reciprocal space plane is the Bragg plane. | 1 | Crystallography |
Crystals can be classified in three ways: lattice systems, crystal systems and crystal families. The various classifications are often confused: in particular the trigonal crystal system is often confused with the rhombohedral lattice system, and the term "crystal system" is sometimes used to mean "lattice system" or "crystal family". | 1 | Crystallography |
The van Deemter equation in chromatography, named for Jan van Deemter, relates the variance per unit length of a separation column to the linear mobile phase velocity by considering physical, kinetic, and thermodynamic properties of a separation. These properties include pathways within the column, diffusion (axial and longitudinal), and mass transfer kinetics between stationary and mobile phases. In liquid chromatography, the mobile phase velocity is taken as the exit velocity, that is, the ratio of the flow rate in ml/second to the cross-sectional area of the ‘column-exit flow path.’ For a packed column, the cross-sectional area of the column exit flow path is usually taken as 0.6 times the cross-sectional area of the column. Alternatively, the linear velocity can be taken as the ratio of the column length to the dead time. If the mobile phase is a gas, then the pressure correction must be applied. The variance per unit length of the column is taken as the ratio of the column length to the column efficiency in theoretical plates. The van Deemter equation is a hyperbolic function that predicts that there is an optimum velocity at which there will be the minimum variance per unit column length and, thence, a maximum efficiency. The van Deemter equation was the result of the first application of rate theory to the chromatography elution process. | 0 | Chromatography + Titration + pH indicators |
* First position – primary direction – z direction, assigned to the higher-order axis.
* Second position – symmetrically equivalent secondary directions, which are perpendicular to the z-axis. These can be 2, m, or
* Third position – symmetrically equivalent tertiary directions, passing between secondary directions. These can be 2, m, or
These are the crystallographic groups 3, 32, 3m, , and (trigonal crystal system), 4, 422, 4mm, , 2m, , and (tetragonal), and 6, 622, 6mm, , m2, , and (hexagonal). Analogously, symbols of non-crystallographic groups (with axes of order 5, 7, 8, 9, ...) can be constructed. These groups can be arranged in the following table
It can be noticed that in groups with odd-order axes n and the third position in symbol is always absent, because all n directions, perpendicular to higher-order axis, are symmetrically equivalent. For example, in the picture of a triangle all three mirror planes (S, S, S) are equivalent – all of them pass through one vertex and the center of the opposite side.
For even-order axes n and there are secondary directions and tertiary directions. For example, in the picture of a regular hexagon one can distinguish two sets of mirror planes – three planes go through two opposite vertexes, and three other planes go through the centers of opposite sides. In this case any of two sets can be chosen as secondary directions, the rest set will be tertiary directions. Hence groups 2m, 2m, 2m, ... can be written as m2, m2, m2, ... . For symbols of point groups this order usually doesnt matter; however, it will be important for Hermann–Mauguin symbols of corresponding space groups, where secondary directions are directions of symmetry elements along unit cell translations b and c, while the tertiary directions correspond to the direction between unit cell translations b and c. For example, symbols Pm2 and P2m denote two different space groups. This also applies to symbols of space groups with odd-order axes 3 and . The perpendicular symmetry elements can go along unit cell translations b and c' or between them. Space groups P321 and P312 are examples of the former and the latter cases, respectively.
The symbol of point group may be confusing; the corresponding Schoenflies symbol is D, which means that the group consists of 3-fold axis, three perpendicular 2-fold axes, and 3 vertical diagonal planes passing between these 2-fold axes, so it seems that the group can be denoted as 32m or 3m2. However, one should remember that, unlike Schoenflies notation, the direction of a plane in a Hermann–Mauguin symbol is defined as the direction perpendicular to the plane, and in the D group all mirror planes are perpendicular to 2-fold axes, so they should be written in the same position as . Second, these complexes generate an inversion center, which combining with the 3-fold rotation axis generates a rotoinversion axis.
Groups with n = ∞ are called limit groups or Curie groups. | 1 | Crystallography |
The phenolic metabolic pathways and enzymes may be studied by mean of transgenesis of genes. The Arabidopsis regulatory gene in the production of anthocyanin pigment 1 (AtPAP1) may be expressed in other plant species. | 0 | Chromatography + Titration + pH indicators |
Liquid-phase epitaxy (LPE) is a method to grow semiconductor crystal layers from the melt on solid substrates. This happens at temperatures well below the melting point of the deposited semiconductor. The semiconductor is dissolved in the melt of another material. At conditions that are close to the equilibrium between dissolution and deposition, the deposition of the semiconductor crystal on the substrate is relatively fast and uniform. The most used substrate is indium phosphide (InP). Other substrates like glass or ceramic can be applied for special applications. To facilitate nucleation, and to avoid tension in the grown layer the thermal expansion coefficient of substrate and grown layer should be similar.
Centrifugal liquid-phase epitaxy is used commercially to make thin layers of silicon, germanium, and gallium arsenide. Centrifugally formed film growth is a process used to form thin layers of materials by using a centrifuge. The process has been used to create silicon for thin-film solar cells and far-infrared photodetectors. Temperature and centrifuge spin rate are used to control layer growth. Centrifugal LPE has the capability to create dopant concentration gradients while the solution is held at constant temperature. | 1 | Crystallography |
LaAlO doped with neodymium gave laser emission at 1080 nm. Mixed methylammonium lead halide () cells fashioned into optically pumped vertical-cavity surface-emitting lasers (VCSELs) convert visible pump light to near-IR laser light with a 70% efficiency. | 1 | Crystallography |
Using matrix matched calibration standards can compensate for ion suppression. Using this technique, calibration standards are prepared in identical sample matrix to that used for analysis (e.g. plasma) by spiking a normal sample with known concentrations of analyte. This is not always possible for biological samples, since the analyte of interest is often endogenously present in a clinically significant, albeit normal, quantity. For matrix matched calibration standards to be effective in compensating for ion suppression, the sample matrix must be free of the analyte of interest. Additionally, it is important that there is little variation in test sample composition since both the test sample and the prepared calibration sample must be affected in the same way by ion suppression. Again, in complex biological samples from different individuals, or even the same individual at a different time, there may be large fluctuations in the concentrations of ion suppressing species. | 0 | Chromatography + Titration + pH indicators |
Crystal chemistry is the study of the principles of chemistry behind crystals and their use in describing structure-property relations in solids, as well as the chemical properties of periodic structures. The principles that govern the assembly of crystal and glass structures are described, models of many of the technologically important crystal structures (alumina, quartz, perovskite) are studied, and the effect of crystal structure on the various fundamental mechanisms responsible for many physical properties are discussed.
The objectives of the field include:
#identifying important raw materials and minerals as well as their names and chemical formulae.
#describing the crystal structure of important materials and determining their atomic details
#learning the systematics of crystal and glass chemistry.
#understanding how physical and chemical properties are related to crystal structure and microstructure.
#studying the engineering significance of these ideas and how they relate to foreign products: past, present, and future.
Topics studied are:
#Chemical bonding, Electronegativity
#Fundamentals of crystallography: crystal systems, Miller Indices, symmetry elements, bond lengths and radii, theoretical density
#Crystal and glass structure prediction: Pauling's and Zachariasen’s rules
#Phase diagrams and crystal chemistry (including solid solutions)
#Imperfections (including defect chemistry and line defects)
#Phase transitions
#Structure – property relations: Neumann's law, melting point, mechanical properties (hardness, slip, cleavage, elastic moduli), wetting, thermal properties (thermal expansion, specific heat, thermal conductivity), diffusion, ionic conductivity, refractive index, absorption, color, Dielectrics and Ferroelectrics, and Magnetism
#Crystal structures of representative metals, semiconductors, polymers, and ceramics | 1 | Crystallography |
Kapustinskii originally proposed the following simpler form, which he faulted as "associated with antiquated concepts of the character of repulsion forces".
Here, K. This form of the Kapustinskii equation may be derived as an approximation of the Born–Landé equation, below.
Kapustinskii replaced r, the measured distance between ions, with the sum of the corresponding ionic radii. In addition, the Born exponent, n, was assumed to have a mean value of 9. Finally, Kapustinskii noted that the Madelung constant, M, was approximately 0.88 times the number of ions in the empirical formula. The derivation of the later form of the Kapustinskii equation followed similar logic, starting from the quantum chemical treatment in which the final term is where d is as defined above. Replacing r as before yields the full Kapustinskii equation. | 1 | Crystallography |
Twenty of the 32 crystal classes are piezoelectric, and crystals belonging to one of these classes (point groups) display piezoelectricity. All piezoelectric classes lack inversion symmetry. Any material develops a dielectric polarization when an electric field is applied, but a substance that has such a natural charge separation even in the absence of a field is called a polar material. Whether or not a material is polar is determined solely by its crystal structure. Only 10 of the 32 point groups are polar. All polar crystals are pyroelectric, so the 10 polar crystal classes are sometimes referred to as the pyroelectric classes.
There are a few crystal structures, notably the perovskite structure, which exhibit ferroelectric behavior. This is analogous to ferromagnetism, in that, in the absence of an electric field during production, the ferroelectric crystal does not exhibit a polarization. Upon the application of an electric field of sufficient magnitude, the crystal becomes permanently polarized. This polarization can be reversed by a sufficiently large counter-charge, in the same way that a ferromagnet can be reversed. However, although they are called ferroelectrics, the effect is due to the crystal structure (not the presence of a ferrous metal). | 1 | Crystallography |
Titration (also known as titrimetry and volumetric analysis) is a common laboratory method of quantitative chemical analysis to determine the concentration of an identified analyte (a substance to be analyzed). A reagent, termed the titrant or titrator, is prepared as a standard solution of known concentration and volume. The titrant reacts with a solution of analyte (which may also be termed the titrand) to determine the analytes concentration. The volume of titrant that reacted with the analyte is termed the titration volume'. | 0 | Chromatography + Titration + pH indicators |
In 1989, Alan Mackay suggested that if chemical synthesis could be used to make L-protein and D-protein enantiomers, it would enable the use of racemic mixtures to crystallize proteins in centrosymmetric space groups. He stated that, because in the X-ray diffraction data obtained from a centrosymmetric crystal the off-diagonal phases would cancel giving phases that differ by 180 degrees, this would facilitate solving the phase problem in protein structure determination through X-ray crystallography.
In 1993, Laura Zawadzke and Jeremy Berg first used the small (45 amino acids) protein rubredoxin to synthesize it in racemic form. This was done since the structural determination would potentially be easier and more robust by using diffraction data from a centrosymmetric crystal, which requires growth from a racemic mixture. By having a centre of symmetry formed by the racemic protein pairs, the steps of phasing diffraction in data analysis would be further simplified. As mentioned above, in 1995 Stephanie Wukovitz and Todd Yeates had developed a mathematical theory to explain why protein molecules tend to crystallize more frequently in certain space groups than in others; they predicted that the most favored protein space group would be P1<bar>, and predicted that globular proteins would crystallize more easily as racemates, from a racemic protein mixture. | 1 | Crystallography |
* EAS Award for Outstanding Achievements in the Fields of Analytical Chemistry (2023)
* Martin Medal (2019)
* Ralph N. Adams Award in Bioanalyical Chemistry (2016)
* ACS Award in Chromatography (2017)
* CASSS Award for Outstanding Achievements in Separation Science (2017)
* Marcel Golay Award for Lifetime Achievement in Capillary Chromatography (2012)
* Eastern Analytical Symposium Award for Separation Science (2012)
* McKnight Award for Technical Innovations in Neuroscience (2010)
* Rackham Distinguished Faculty Achievement Award (2009)
* American Microchemical Society’s Benedetti-Pichler Memorial Award (2001) | 0 | Chromatography + Titration + pH indicators |
In crystallography and solid state physics, the Laue equations relate incoming waves to outgoing waves in the process of elastic scattering, where the photon energy or light temporal frequency does not change upon scattering by a crystal lattice. They are named after physicist Max von Laue (1879–1960).
The Laue equations can be written as as the condition of elastic wave scattering by a crystal lattice, where is the scattering vector, , are incoming and outgoing wave vectors (to the crystal and from the crystal, by scattering), and is a crystal reciprocal lattice vector. Due to elastic scattering , three vectors. , , and , form a rhombus if the equation is satisfied. If the scattering satisfies this equation, all the crystal lattice points scatter the incoming wave toward the scattering direction (the direction along ). If the equation is not satisfied, then for any scattering direction, only some lattice points scatter the incoming wave. (This physical interpretation of the equation is based on the assumption that scattering at a lattice point is made in a way that the scattering wave and the incoming wave have the same phase at the point.) It also can be seen as the conservation of momentum as since is the wave vector for a plane wave associated with parallel crystal lattice planes. (Wavefronts of the plane wave are coincident with these lattice planes.)
The equations are equivalent to Braggs law; the Laue equations are vector equations while Braggs law is in a form that is easier to solve, but these tell the same content. | 1 | Crystallography |
Since its inception as a tool of analytical chemistry, LC-MS/MS spread rapidly and indeed continues to do so in (amongst others) bioanalytical fields. One of the advantages of the technique is its selectivity for many analytes of interest. However, this high selectivity could lead to a misconception that it is always possible to simplify or (on occasion) almost completely remove the necessity for extensive sample preparation. However, during and after uptake by bioanalytical laboratories worldwide, it became apparent that there were inherent problems with detection of relatively small analyte concentrations in the complex sample matrices associated with biological fluids (e.g. blood and urine). | 0 | Chromatography + Titration + pH indicators |
In two dimensions, any lattice can be specified by the length of its two primitive translation vectors and the angle between them. There are an infinite number of possible lattices one can describe in this way. Some way to categorize different types of lattices is desired. One way to do so is to recognize that some lattices have inherent symmetry. One can impose conditions on the length of the primitive translation vectors and on the angle between them to produce various symmetric lattices. These symmetries themselves are categorized into different types, such as point groups (which includes mirror symmetries, inversion symmetries and rotation symmetries) and translational symmetries. Thus, lattices can be categorized based on what point group or translational symmetry applies to them.
In two dimensions, the most basic point group corresponds to rotational invariance under 2π and π, or 1- and 2-fold rotational symmetry. This actually applies automatically to all 2D lattices, and is the most general point group. Lattices contained in this group (technically all lattices, but conventionally all lattices that don't fall into any of the other point groups) are called oblique lattices. From there, there are 4 further combinations of point groups with translational elements (or equivalently, 4 types of restriction on the lengths/angles of the primitive translation vectors) that correspond to the 4 remaining lattice categories: square, hexagonal, rectangular, and centered rectangular. Thus altogether there are 5 Bravais lattices in 2 dimensions.
Likewise, in 3 dimensions, there are 14 Bravais lattices: 1 general "wastebasket" category (triclinic) and 13 more categories. These 14 lattice types are classified by their point groups into 7 lattice systems (triclinic, monoclinic, orthorhombic, tetragonal, cubic, rhombohedral, and hexagonal). | 1 | Crystallography |
The anthocyanins, anthocyanidins with sugar group(s), are mostly 3-glucosides of the anthocyanidins. The anthocyanins are subdivided into the sugar-free anthocyanidin aglycones and the anthocyanin glycosides. As of 2003, more than 400 anthocyanins had been reported, while later literature in early 2006, puts the number at more than 550 different anthocyanins. The difference in chemical structure that occurs in response to changes in pH, is the reason why anthocyanins often are used as pH indicators, as they change from red in acids to blue in bases through a process called halochromism. | 0 | Chromatography + Titration + pH indicators |
Goldschmidts tolerance factor (from the German word Toleranzfaktor') is an indicator for the stability and distortion of crystal structures. It was originally only used to describe the perovskite ABO structure, but now tolerance factors are also used for ilmenite.
Alternatively the tolerance factor can be used to calculate the compatibility of an ion with a crystal structure.
The first description of the tolerance factor for perovskite was made by Victor Moritz Goldschmidt in 1926. | 1 | Crystallography |
Thermometric titrimetry is particularly suited to the determination of a range of analytes where a precipitate is formed by reaction with the titrant. In some cases, an alternative to traditional potentiometric titration practice can be offered. In other cases, reaction chemistries may be employed for which there is no satisfactory equivalent in potentiometric titrimetry. | 0 | Chromatography + Titration + pH indicators |
Liquid chromatography is a method of physical separation in which the components of a liquid mixture are distributed between two immiscible phases, i.e., stationary and mobile. The practice of LC can be divided into five categories, i.e., adsorption chromatography, partition chromatography, ion-exchange chromatography, size-exclusion chromatography, and affinity chromatography. Among these, the most widely used variant is the reverse-phase (RP) mode of the partition chromatography technique, which makes use of a nonpolar (hydrophobic) stationary phase and a polar mobile phase. In common applications, the mobile phase is a mixture of water and other polar solvents (e.g., methanol, isopropanol, and acetonitrile), and the stationary matrix is prepared by attaching long-chain alkyl groups (e.g., n-octadecyl or C) to the external and internal surfaces of irregularly or spherically shaped 5 μm diameter porous silica particles.
In HPLC, typically 20 μl of the sample of interest are injected into the mobile phase stream delivered by a high pressure pump. The mobile phase containing the analytes permeates through the stationary phase bed in a definite direction. The components of the mixture are separated depending on their chemical affinity with the mobile and stationary phases. The separation occurs after repeated sorption and desorption steps occurring when the liquid interacts with the stationary bed. The liquid solvent (mobile phase) is delivered under high pressure (up to 400 bar or 5800 psi) into a packed column containing the stationary phase. The high pressure is necessary to achieve a constant flow rate for reproducible chromatography experiments. Depending on the partitioning between the mobile and stationary phases, the components of the sample will flow out of the column at different times. The column is the most important component of the LC system and is designed to withstand the high pressure of the liquid. Conventional LC columns are 100–300 mm long with outer diameter of 6.4 mm (1/4 inch) and internal diameter of 3.0–4.6 mm. For applications involving LC–MS, the length of chromatography columns can be shorter (30–50 mm) with 3–5 μm diameter packing particles. In addition to the conventional model, other LC columns are the narrow bore, microbore, microcapillary, and nano-LC models. These columns have smaller internal diameters, allow for a more efficient separation, and handle liquid flows under 1 ml/min (the conventional flow-rate). In order to improve separation efficiency and peak resolution, ultra performance liquid chromatography (UHPLC) can be used instead of HPLC. This LC variant uses columns packed with smaller silica particles (~1.7 μm diameter) and requires higher operating pressures in the range of 310000 to 775000 torr (6000 to 15000 psi, 400 to 1034 bar). | 0 | Chromatography + Titration + pH indicators |
Zone axis, a term sometimes used to refer to "high-symmetry" orientations in a crystal, most generally refers to any direction referenced to the direct lattice (as distinct from the reciprocal lattice) of a crystal in three dimensions. It is therefore indexed with direct lattice indices, instead of with Miller indices.
High-symmetry zone axes through a crystal lattice, in particular, often lie in the direction of tunnels through the crystal between planes of atoms. This is because, as we see below, such zone axis directions generally lie within more than one plane of atoms in the crystal. | 1 | Crystallography |
The Green-Kubo relations can be used to calculate the thermal transport properties of a mineral. Since the velocities of the ions are stored at each numerical step, one can calculate the time correlation of later velocities with earlier velocities. The integral of these correlations is related to the Fourier thermal coefficient. | 1 | Crystallography |
Quinaldine red is an indicator that turns from colorless to red between a pH of 1.0–2.2. The image below shows what color quinaldine red would appear as in a given pH.
It is a cationic molecule that undergoes oxidation at different levels of pH. The rate of oxidation of Quinaldine red is in the first order with respect to the concentration of the oxidizing agent.
Other factors that increases the rate of oxidation includes increasing pH and increased sodium carbonate concentration. The reaction rate eventually levels off due to the maximum formation of the product within the oxidation process.
Quinaldine red also has the ability to fluoresce. Free quinaldine red does not fluoresce in solution when it is not bound to anything, making quinaldine red only visible by fluorescence when it is bound to something. Quinaldine red can exhibit fluorescence when it is bound to nucleic acids, which then emit radiation between 580-650 nm.
Maximum fluorescence of QR is detected from 557 nm to 607 nm. QR and the nucleic acids react quickly under room temperature, and the resulting QR-nucleic acid complex is able to fluorescence. However, fluorescent activity decrease as time goes on. Maximum fluorescence between QR and DNA is found within the pH range of 3.2-3.6, with the optimum being a pH 3.5. The amount of fluorescence seen with the use of QR is linearly related to the concentrations of DNA or RNA. | 0 | Chromatography + Titration + pH indicators |
Very small amount of carbon is sufficient to stabilize "ScBC". This compound has a broad composition range, namely ScBC with x ≤ 2.2 and y ≤ 0.44. ScBC has a hexagonal crystal structure with space group P6mmm (No. 199) and lattice constants a, b = 1.45501(15) nm and c = 0.84543(16) nm.
There are 19 atomic sites in the unit cell, which are assigned to one scandium site Sc, 14 boron sites B1–B14 having 100% occupancy, two boron-carbon mixed-occupancy sites B/C15 and B/C16, and two partial-occupancy boron sites B17 and B18. Atomic coordinates, site occupancies and isotropic displacement factors are listed in table VII. Although a very small amount of carbon (less than 2 wt%!) plays an important role in the phase stability, carbon does not have its own sites but shares with boron two interstitial sites B/C15 and B/C16.
There are two inequivalent B icosahedra, I1 and I2, which are constructed by the B1–B5 and B8–B12 sites, respectively. A "tube" is another characteristic structure unit of ScBC. It extends along the c-axis and consists of B13, B14, B17 and B18 sites where B13 and B14 form 6-membered rings. B17 and B18 sites also form 6-membered rings; however, their mutual distances (0.985 Å for B17 and 0.955 Å for B18) are too short for a simultaneous occupation of the neighboring sites. Therefore, boron atoms occupy 2nd neighbor site forming a triangle. The occupancies of B17 and B18 sites should be 50%, but the structure analysis suggests larger values. The crystal structure viewed along the a-axis is shown in figure 20, which suggests that the ScBC is a layered material. Two layers, respectively constructed by the icosahedra I1 and I2, alternatively stack along the c-axis. However, the ScBC crystal is not layered. For example, during arc-melting, ScBC needle crystals violently grow along the c-axis – this never happens in layered compounds. The crystal structure viewed along the c-axis is shown in figure 21a. The icosahedra I1 and I2 form a ring centered by the "tube" shown in figure 21b, which probably governs the properties of the ScBC crystal. B/C15 and B/C16 mixed-occupancy sites interconnect the rings. A structural similarity can be seen between ScBC and BeB.
Figures 22a and b present HRTEM lattice images and electron diffraction patterns taken along the [0001] and [110] crystalline directions, respectively. The HRTEM lattice image of figure 22a reproduces well the (a, b) plane of the crystal structure shown in figure 21a, with the clearly visible rings membered by icosahedra I1 and I2 and centered by the "tube". Figure 22b proves that ScBC does not have layered character but its c-axis direction is built up by the ring-like structure and tubular structures. | 1 | Crystallography |
In polymer systems, the general definition () holds; the elementary constituents are now the monomers making up the chains. However, the structure factor being a measure of the correlation between particle positions, one can reasonably expect that this correlation will be different for monomers belonging to the same chain or to different chains.
Let us assume that the volume contains identical molecules, each composed of monomers, such that ( is also known as the degree of polymerization). We can rewrite () as:
where indices label the different molecules and the different monomers along each molecule. On the right-hand side we separated intramolecular () and intermolecular () terms. Using the equivalence of the chains, () can be simplified:
where is the single-chain structure factor. | 1 | Crystallography |
In crystallography, the Sayre equation, named after David Sayre who introduced it in 1952, is a mathematical relationship that allows one to calculate probable values for the phases of some diffracted beams. It is used when employing direct methods to solve a structure. Its formulation is the following:
which states how the structure factor for a beam can be calculated as the sum of the products of pairs of structure factors whose indices sum to the desired values of . Since weak diffracted beams will contribute a little to the sum, this method can be a powerful way of finding the phase of related beams, if some of the initial phases are already known by other methods.
In particular, for three such related beams in a centrosymmetric structure, the phases can only be 0 or and the Sayre equation reduces to the triplet relationship:
where the indicates the sign of the structure factor (positive if the phase is 0 and negative if it is ) and the sign indicates that there is a certain degree of probability that the relationship is true, which becomes higher the stronger the beams are. | 1 | Crystallography |
It is a possible carcinogen. As "butter yellow", the agent had been used as a food additive in butter and margarine before its toxicity was recognized. | 0 | Chromatography + Titration + pH indicators |
Protein crystallization is the process of formation of a regular array of individual protein molecules stabilized by crystal contacts. If the crystal is sufficiently ordered, it will diffract. Some proteins naturally form crystalline arrays, like aquaporin in the lens of the eye.
In the process of protein crystallization, proteins are dissolved in an aqueous environment and sample solution until they reach the supersaturated state. Different methods are used to reach that state such as vapor diffusion, microbatch, microdialysis, and free-interface diffusion. Developing protein crystals is a difficult process influenced by many factors, including pH, temperature, ionic strength in the crystallization solution, and even gravity. Once formed, these crystals can be used in structural biology to study the molecular structure of the protein, particularly for various industrial or medical purposes. | 1 | Crystallography |
IUPAC defines the temperature programmed chromatography Kovats index equation:
* & retention times of trailing and heading n-alkanes, respectively.
NOTE: TPGC index does depend on temperature program, gas velocity and the column used !
ASTM method D6730 defines the temperature programmed chromatography Kovats index equation:
Measured Kovats retention index values can be found in ASTM method D 6730 databases.
An extensive Kovats index database is compiled by NIST [https://webbook.nist.gov/chemistry/].
The equations produce significant different Kovats indices. | 0 | Chromatography + Titration + pH indicators |