1.
Jmol
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Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool and it is written in the programming language Java, so it can run on the operating systems Windows, macOS, Linux, and Unix, if Java is installed. It is free and open-source software released under a GNU Lesser General Public License version 2.0, a standalone application and a software development kit exist that can be integrated into other Java applications, such as Bioclipse and Taverna. A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways, for example, molecules can be displayed as ball-and-stick models, space-filling models, ribbon diagrams, etc. Jmol supports a range of chemical file formats, including Protein Data Bank, Crystallographic Information File, MDL Molfile. There is also a JavaScript-only version, JSmol, that can be used on computers with no Java, the Jmol applet, among other abilities, offers an alternative to the Chime plug-in, which is no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS9. Jmol requires Java installation and operates on a variety of platforms. For example, Jmol is fully functional in Mozilla Firefox, Internet Explorer, Opera, Google Chrome, fast and Scriptable Molecular Graphics in Web Browsers without Java3D
2.
ChemSpider
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ChemSpider is a database of chemicals. ChemSpider is owned by the Royal Society of Chemistry, the database contains information on more than 50 million molecules from over 500 data sources including, Each chemical is given a unique identifier, which forms part of a corresponding URL. This is an approach to develop an online chemistry database. The search can be used to widen or restrict already found results, structure searching on mobile devices can be done using free apps for iOS and for the Android. The ChemSpider database has been used in combination with text mining as the basis of document markup. The result is a system between chemistry documents and information look-up via ChemSpider into over 150 data sources. ChemSpider was acquired by the Royal Society of Chemistry in May,2009, prior to the acquisition by RSC, ChemSpider was controlled by a private corporation, ChemZoo Inc. The system was first launched in March 2007 in a release form. ChemSpider has expanded the generic support of a database to include support of the Wikipedia chemical structure collection via their WiChempedia implementation. A number of services are available online. SyntheticPages is an interactive database of synthetic chemistry procedures operated by the Royal Society of Chemistry. Users submit synthetic procedures which they have conducted themselves for publication on the site and these procedures may be original works, but they are more often based on literature reactions. Citations to the published procedure are made where appropriate. They are checked by an editor before posting. The pages do not undergo formal peer-review like a journal article. The comments are moderated by scientific editors. The intention is to collect practical experience of how to conduct useful chemical synthesis in the lab, while experimental methods published in an ordinary academic journal are listed formally and concisely, the procedures in ChemSpider SyntheticPages are given with more practical detail. Comments by submitters are included as well, other publications with comparable amounts of detail include Organic Syntheses and Inorganic Syntheses
3.
PubChem
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PubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information, a component of the National Library of Medicine, PubChem can be accessed for free through a web user interface. Millions of compound structures and descriptive datasets can be downloaded via FTP. PubChem contains substance descriptions and small molecules with fewer than 1000 atoms and 1000 bonds, more than 80 database vendors contribute to the growing PubChem database. PubChem consists of three dynamically growing primary databases, as of 28 January 2016, Compounds,82.6 million entries, contains pure and characterized chemical compounds. Substances,198 million entries, contains also mixtures, extracts, complexes, bioAssay, bioactivity results from 1.1 million high-throughput screening programs with several million values. PubChem contains its own online molecule editor with SMILES/SMARTS and InChI support that allows the import and export of all common chemical file formats to search for structures and fragments. In the text search form the database fields can be searched by adding the name in square brackets to the search term. A numeric range is represented by two separated by a colon. The search terms and field names are case-insensitive, parentheses and the logical operators AND, OR, and NOT can be used. AND is assumed if no operator is used, example,0,5000,50,10 -5,5 PubChem was released in 2004. The American Chemical Society has raised concerns about the publicly supported PubChem database and they have a strong interest in the issue since the Chemical Abstracts Service generates a large percentage of the societys revenue. To advocate their position against the PubChem database, ACS has actively lobbied the US Congress, soon after PubChems creation, the American Chemical Society lobbied U. S. Congress to restrict the operation of PubChem, which they asserted competes with their Chemical Abstracts Service
4.
International Chemical Identifier
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Initially developed by IUPAC and NIST from 2000 to 2005, the format and algorithms are non-proprietary. The continuing development of the standard has supported since 2010 by the not-for-profit InChI Trust. The current version is 1.04 and was released in September 2011, prior to 1.04, the software was freely available under the open source LGPL license, but it now uses a custom license called IUPAC-InChI Trust License. Not all layers have to be provided, for instance, the layer can be omitted if that type of information is not relevant to the particular application. InChIs can thus be seen as akin to a general and extremely formalized version of IUPAC names and they can express more information than the simpler SMILES notation and differ in that every structure has a unique InChI string, which is important in database applications. Information about the 3-dimensional coordinates of atoms is not represented in InChI, the InChI algorithm converts input structural information into a unique InChI identifier in a three-step process, normalization, canonicalization, and serialization. The InChIKey, sometimes referred to as a hashed InChI, is a fixed length condensed digital representation of the InChI that is not human-understandable. The InChIKey specification was released in September 2007 in order to facilitate web searches for chemical compounds and it should be noted that, unlike the InChI, the InChIKey is not unique, though collisions can be calculated to be very rare, they happen. In January 2009 the final 1.02 version of the InChI software was released and this provided a means to generate so called standard InChI, which does not allow for user selectable options in dealing with the stereochemistry and tautomeric layers of the InChI string. The standard InChIKey is then the hashed version of the standard InChI string, the standard InChI will simplify comparison of InChI strings and keys generated by different groups, and subsequently accessed via diverse sources such as databases and web resources. Every InChI starts with the string InChI= followed by the version number and this is followed by the letter S for standard InChIs. The remaining information is structured as a sequence of layers and sub-layers, the layers and sub-layers are separated by the delimiter / and start with a characteristic prefix letter. The six layers with important sublayers are, Main layer Chemical formula and this is the only sublayer that must occur in every InChI. The atoms in the formula are numbered in sequence, this sublayer describes which atoms are connected by bonds to which other ones. Describes how many hydrogen atoms are connected to each of the other atoms, the condensed,27 character standard InChIKey is a hashed version of the full standard InChI, designed to allow for easy web searches of chemical compounds. Most chemical structures on the Web up to 2007 have been represented as GIF files, the full InChI turned out to be too lengthy for easy searching, and therefore the InChIKey was developed. With all databases currently having below 50 million structures, such duplication appears unlikely at present, a recent study more extensively studies the collision rate finding that the experimental collision rate is in agreement with the theoretical expectations. Example, Morphine has the structure shown on the right, as the InChI cannot be reconstructed from the InChIKey, an InChIKey always needs to be linked to the original InChI to get back to the original structure
5.
Simplified molecular-input line-entry system
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The simplified molecular-input line-entry system is a specification in form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules, the original SMILES specification was initiated in the 1980s. It has since modified and extended. In 2007, a standard called OpenSMILES was developed in the open-source chemistry community. Other linear notations include the Wiswesser Line Notation, ROSDAL and SLN, the original SMILES specification was initiated by David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s. The Environmental Protection Agency funded the project to develop SMILES. It has since modified and extended by others, most notably by Daylight Chemical Information Systems. In 2007, a standard called OpenSMILES was developed by the Blue Obelisk open-source chemistry community. Other linear notations include the Wiswesser Line Notation, ROSDAL and SLN, in July 2006, the IUPAC introduced the InChI as a standard for formula representation. SMILES is generally considered to have the advantage of being slightly more human-readable than InChI, the term SMILES refers to a line notation for encoding molecular structures and specific instances should strictly be called SMILES strings. However, the term SMILES is also used to refer to both a single SMILES string and a number of SMILES strings, the exact meaning is usually apparent from the context. The terms canonical and isomeric can lead to confusion when applied to SMILES. The terms describe different attributes of SMILES strings and are not mutually exclusive, typically, a number of equally valid SMILES strings can be written for a molecule. For example, CCO, OCC and CC all specify the structure of ethanol, algorithms have been developed to generate the same SMILES string for a given molecule, of the many possible strings, these algorithms choose only one of them. This SMILES is unique for each structure, although dependent on the algorithm used to generate it. These algorithms first convert the SMILES to a representation of the molecular structure. A common application of canonical SMILES is indexing and ensuring uniqueness of molecules in a database, there is currently no systematic comparison across commercial software to test if such flaws exist in those packages. SMILES notation allows the specification of configuration at tetrahedral centers, and these are structural features that cannot be specified by connectivity alone and SMILES which encode this information are termed isomeric SMILES
6.
Chemical formula
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These are limited to a single typographic line of symbols, which may include subscripts and superscripts. A chemical formula is not a name, and it contains no words. Although a chemical formula may imply certain simple chemical structures, it is not the same as a full chemical structural formula. Chemical formulas can fully specify the structure of only the simplest of molecules and chemical substances, the simplest types of chemical formulas are called empirical formulas, which use letters and numbers indicating the numerical proportions of atoms of each type. Molecular formulas indicate the numbers of each type of atom in a molecule. For example, the formula for glucose is CH2O, while its molecular formula is C6H12O6. This is possible if the relevant bonding is easy to show in one dimension, an example is the condensed molecular/chemical formula for ethanol, which is CH3-CH2-OH or CH3CH2OH. For reasons of structural complexity, there is no condensed chemical formula that specifies glucose, chemical formulas may be used in chemical equations to describe chemical reactions and other chemical transformations, such as the dissolving of ionic compounds into solution. A chemical formula identifies each constituent element by its chemical symbol, in empirical formulas, these proportions begin with a key element and then assign numbers of atoms of the other elements in the compound, as ratios to the key element. For molecular compounds, these numbers can all be expressed as whole numbers. For example, the formula of ethanol may be written C2H6O because the molecules of ethanol all contain two carbon atoms, six hydrogen atoms, and one oxygen atom. Some types of compounds, however, cannot be written with entirely whole-number empirical formulas. An example is boron carbide, whose formula of CBn is a variable non-whole number ratio with n ranging from over 4 to more than 6.5. When the chemical compound of the consists of simple molecules. These types of formulas are known as molecular formulas and condensed formulas. A molecular formula enumerates the number of atoms to reflect those in the molecule, so that the formula for glucose is C6H12O6 rather than the glucose empirical formula. However, except for very simple substances, molecular chemical formulas lack needed structural information, for simple molecules, a condensed formula is a type of chemical formula that may fully imply a correct structural formula. For example, ethanol may be represented by the chemical formula CH3CH2OH
7.
Melting point
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The melting point of a solid is the temperature at which it changes state from solid to liquid at atmospheric pressure. At the melting point the solid and liquid phase exist in equilibrium, the melting point of a substance depends on pressure and is usually specified at standard pressure. When considered as the temperature of the change from liquid to solid. Because of the ability of some substances to supercool, the point is not considered as a characteristic property of a substance. For most substances, melting and freezing points are approximately equal, for example, the melting point and freezing point of mercury is 234.32 kelvins. However, certain substances possess differing solid-liquid transition temperatures, for example, agar melts at 85 °C and solidifies from 31 °C to 40 °C, such direction dependence is known as hysteresis. The melting point of ice at 1 atmosphere of pressure is close to 0 °C. In the presence of nucleating substances the freezing point of water is the same as the melting point, the chemical element with the highest melting point is tungsten, at 3687 K, this property makes tungsten excellent for use as filaments in light bulbs. Many laboratory techniques exist for the determination of melting points, a Kofler bench is a metal strip with a temperature gradient. Any substance can be placed on a section of the strip revealing its thermal behaviour at the temperature at that point, differential scanning calorimetry gives information on melting point together with its enthalpy of fusion. A basic melting point apparatus for the analysis of crystalline solids consists of an oil bath with a transparent window, the several grains of a solid are placed in a thin glass tube and partially immersed in the oil bath. The oil bath is heated and with the aid of the melting of the individual crystals at a certain temperature can be observed. In large/small devices, the sample is placed in a heating block, the measurement can also be made continuously with an operating process. For instance, oil refineries measure the point of diesel fuel online, meaning that the sample is taken from the process. This allows for more frequent measurements as the sample does not have to be manually collected, for refractory materials the extremely high melting point may be determined by heating the material in a black body furnace and measuring the black-body temperature with an optical pyrometer. For the highest melting materials, this may require extrapolation by several hundred degrees, the spectral radiance from an incandescent body is known to be a function of its temperature. An optical pyrometer matches the radiance of a body under study to the radiance of a source that has been previously calibrated as a function of temperature, in this way, the measurement of the absolute magnitude of the intensity of radiation is unnecessary. However, known temperatures must be used to determine the calibration of the pyrometer, for temperatures above the calibration range of the source, an extrapolation technique must be employed
8.
Solubility
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Solubility is the property of a solid, liquid, or gaseous chemical substance called solute to dissolve in a solid, liquid, or gaseous solvent. The solubility of a substance depends on the physical and chemical properties of the solute and solvent as well as on temperature, pressure. The solubility of a substance is a different property from the rate of solution. Most often, the solvent is a liquid, which can be a substance or a mixture. One may also speak of solid solution, but rarely of solution in a gas, the extent of solubility ranges widely, from infinitely soluble such as ethanol in water, to poorly soluble, such as silver chloride in water. The term insoluble is often applied to poorly or very poorly soluble compounds, a common threshold to describe something as insoluble is less than 0.1 g per 100 mL of solvent. Under certain conditions, the solubility can be exceeded to give a so-called supersaturated solution. Metastability of crystals can also lead to apparent differences in the amount of a chemical that dissolves depending on its form or particle size. A supersaturated solution generally crystallises when seed crystals are introduced and rapid equilibration occurs, phenylsalicylate is one such simple observable substance when fully melted and then cooled below its fusion point. Solubility is not to be confused with the ability to dissolve a substance, for example, zinc dissolves in hydrochloric acid as a result of a chemical reaction releasing hydrogen gas in a displacement reaction. The zinc ions are soluble in the acid, the smaller a particle is, the faster it dissolves although there are many factors to add to this generalization. Crucially solubility applies to all areas of chemistry, geochemistry, inorganic, physical, organic, in all cases it will depend on the physical conditions and the enthalpy and entropy directly relating to the solvents and solutes concerned. By far the most common solvent in chemistry is water which is a solvent for most ionic compounds as well as a range of organic substances. This is a factor in acidity/alkalinity and much environmental and geochemical work. According to the IUPAC definition, solubility is the composition of a saturated solution expressed as a proportion of a designated solute in a designated solvent. Solubility may be stated in units of concentration such as molarity, molality, mole fraction, mole ratio, mass per volume. Solubility occurs under dynamic equilibrium, which means that solubility results from the simultaneous and opposing processes of dissolution, the solubility equilibrium occurs when the two processes proceed at a constant rate. The term solubility is used in some fields where the solute is altered by solvolysis
9.
Cyanine
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Cyanine is the non-systematic name of a synthetic dye family belonging to polymethine group. Cyanines were and are used in industry, and more recently in biotechnology. Cyanines have many uses as fluorescent dyes, particularly in biomedical imaging, depending on the structure, they cover the spectrum from IR to UV. There are a number reported in the literature. Both nitrogens are each part of a heteroaromatic moiety, such as pyrrole, imidazole, thiazole, pyridine, quinoline, indole, benzothiazole. Cyanines were first synthesized over a century ago, cyanines are also used in CD-R and DVD-R media. The ones used are green or light blue in color. These discs are often rated with a life of 75 years or more. The other dyes used in CD-Rs are phthalocyanine and azo, labeling is done for visualization and quantification purposes. Cyanines dyes are available with different modifications such as methyl, ethyl or butyl substituent, carboxyl, acetylmethoxy, Cy 3 and Cy5 are the most popular, used typically combined for 2 colors detection. Cy3 fluoresces greenish yellow, while Cy5 is fluorescent in the red region, Cy3 can be detected by various fluorometers, imagers, and microscopes with standard filters for Tetramethylrhodamine. Due to inherently high extinction coefficient, this dye is also detected by naked eye on gels. The scanners actually use different laser emission wavelengths and filter wavelengths to avoid background contamination and they are thus able to easily distinguish colors from Cy3 and from Cy5, and also able to quantify the amount of Cy3 and Cy5 labeling in one sample. Other cyanine dyes are useful, Cy3.5 can replace SulfoRhodamine 101, Cy5.5 is a near-infrared fluorescence-emitting dye. Cy7 is a near-IR fluor that is invisible to the naked eye and it is used in in vivo imaging applications, as well as the Cy7.5 dye. Sulfo–Cyanine dyes bear classically one or two Sulfo groups, rendering the Cy dye water-soluble, but tri- and quadri-sulfonated forms are available for even higher hydrosolubility, pEGylation is another modification that confers hydrophilicity, not only to the dye but also to the labeled conjugate. Standard chemical names specify exactly the structure of the molecule. The Cy3 and Cy5 nomenclature was first proposed by Ernst, et al. in 1989, in the original paper the number designated the count of the methines, and the side chains were unspecified
10.
Dye
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A dye is a colored substance that has an affinity to the substrate to which it is being applied. The dye is applied in an aqueous solution, and may require a mordant to improve the fastness of the dye on the fiber. Both dyes and pigments are colored because they absorb some wavelengths of light more than others, in contrast to dyes, pigments are insoluble and have no affinity for the substrate. Some dyes can be precipitated with a salt to produce a lake pigment. The majority of natural dyes are from plant sources, roots, berries, bark, leaves, and wood, fungi, textile dyeing dates back to the Neolithic period. Throughout history, people have dyed their textiles using common, locally available materials, scarce dyestuffs that produced brilliant and permanent colors such as the natural invertebrate dyes Tyrian purple and crimson kermes were highly prized luxury items in the ancient and medieval world. Plant-based dyes such as woad, indigo, saffron, and madder were raised commercially and were important trade goods in the economies of Asia, across Asia and Africa, patterned fabrics were produced using resist dyeing techniques to control the absorption of color in piece-dyed cloth. Dyes from the New World such as cochineal and logwood were brought to Europe by the Spanish treasure fleets, dyed flax fibers have been found in the Republic of Georgia in a prehistoric cave dated to 36,000 BP. Archaeological evidence shows that, particularly in India and Phoenicia, dyeing has been carried out for over 5,000 years. The dyes were obtained from animal, vegetable or mineral origin, by far the greatest source of dyes has been from the plant kingdom, notably roots, berries, bark, leaves and wood, but only a few have ever been used on a commercial scale. The discovery of synthetic dyes late in the 19th century ended the large-scale market for natural dyes. These dyes are made from synthetic resources such as petroleum by-products, the first human-made organic aniline dye, mauveine, was discovered serendipitously by William Henry Perkin in 1856, the result of a failed attempt at the total synthesis of quinine. Other aniline dyes followed, such as fuchsine, safranine, many thousands of synthetic dyes have since been prepared. These may be natural or synthetic, other than pigmentation, they have a range of applications including organic dye lasers, optical media and camera sensors. This is the basic classification Dyes are classified according to their solubility, acid dyes are water-soluble anionic dyes that are applied to fibers such as silk, wool, nylon and modified acrylic fibers using neutral to acid dye baths. Attachment to the fiber is attributed, at least partly, to salt formation between anionic groups in the dyes and cationic groups in the fiber, acid dyes are not substantive to cellulosic fibers. Most synthetic food colors fall in this category, basic dyes are water-soluble cationic dyes that are mainly applied to acrylic fibers, but find some use for wool and silk. Usually acetic acid is added to the dye bath to help the uptake of the dye onto the fiber, basic dyes are also used in the coloration of paper
11.
Single-molecule experiment
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A single-molecule experiment is an experiment that investigates the properties of individual molecules. Indeed, since the 90s, many techniques for probing individual molecules have been developed, the first single-molecule experiments were patch clamp experiments performed in the 70s, but these were limited to studying ion channels. Biological polymers conformations have been measured using atomic force microscopy, using force spectroscopy, single molecules, usually polymers, can be mechanically stretched and their elastic response recorded in real time. In the gas phase at pressures, single-molecule experiments have been around for decades. One year later Michel Orrit and Jacky Bernard were able to also the detection of the absorption of single molecules by their fluorescence. Many techniques have the ability to observe one molecule at a time, most notably mass spectrometry, where single ions are detected. In addition one of the earliest means of detecting single molecules, came about in the field of ion channels with the development of the patch clamp technique by Erwin Neher and Bert Sakmann. However, the idea of measuring conductance to look at single molecules placed a limitation on the kind of systems which could be observed. Fluorescence is a convenient means of observing one molecule at a time, mostly due to the sensitivity of commercial optical detectors, the most studied protein has been the class of myosin/actin enzymes found in muscle tissues. Through single-molecule techniques the step mechanism has been observed and characterized in many of these proteins, nanomanipulators such as the atomic force microscope are also suited to single-molecule experiments of biological significance, since they work on the same length scale of most biological polymers. Besides, atomic force microscopy is appropriate for the studies of synthetic polymer molecules, AFM provides a unique possibility of 3D visualization of polymer chains. For instance, AFM tapping mode is gentle enough for the recording of adsorbed polyelectrolyte molecules under liquid medium, the location of two-chain-superposition correspond in these experiments to twice the thickness of single chain. At the application of proper scanning parameters, conformation of such molecules remain unchanged for hours that allows the performance of experiments under liquid media having various properties. Furthermore, by controlling the force between the tip and the high resolution images can be obtained. Optical tweezers have also been used to study. Single-molecule fluorescence spectroscopy uses the fluorescence of a molecule for obtaining information on its environment, structure, the technique affords the ability of obtaining information otherwise not available due to ensemble averaging. The results in experiments of individual molecules are two-state trajectories. Specifically, ion channels alternate between conducting and non-conducting classes, which differ in conformation, therefore, the functional state of ion channels can be directly measured with sufficiently sensitive electronics, provided that proper precautions are taken to minimize noise. In turn, each of these classes may be divided into one or more states with direct bearing on the underlying function of the ion channel
12.
Fate mapping
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When carried out at single-cell resolution, this process is termed cell lineage tracing. The first attempts at fate mapping were made by inferences based on the examination of embryos that had fixed, sectioned. The disadvantage of this technique was that observation of single points in time provide only snapshots of what cell movements are actually occurring. Early embryologists thus had to infer which cells became what tissues at later stages, early embryologists used vital dyes to follow movements of individual cells or groups of cells over time in Xenopus frog embryos. The tissue to which the cells contribute would thus be labeled, the first person to develop and use this technique to study cell fate was embryologist Walter Vogt in 1929. Once the cells were effectively labeled, the chip could be removed. With this method, Vogt was able to discern movements of cell populations. Additionally, the cell or cell population of interest must be superficial, the information Vogt gathered from his tracing experiments of distinct cells and populations of cells in Xenopus was then pooled to construct a fate map. The map was a representation of an embryo that has particular regions highlighted which are known to give rise to specific tissues in the adult organism. For instance, in Figure 1, Nile Blue staining of a 32-cell blastula at the side of the animal pole yields a blue-stained brain. All progeny of the cells could later be discerned by staining for HRP using benzidine substrate or visualized by fluorescence microscopy. This technique allowed the experimenter greater control and selectivity over what cell was labeled and traced, however, the opaque character of the HRP stain prevented use of vital dye nuclear counter-stains such as Hoechst 33258 to observe the mitotic state of the injected cells progeny. Also, embryos had to be fixed in order to stain for the HRP, leech embryos injected with the fluorescent tracers could be visualized, and images collected of the same specimen at multiple timepoints, without fixation. The fluorescent tracers could also be combined with nuclear Hoechst staining to visualize the status of the progeny of injected cells. For this purpose, specific cells were ablated by microinjection with Pronase to ablate the cell, the single-cell injection technique is now also in use by researchers studying other model organisms such as Xenopus, Danio rerio, and Caenorhabditis elegans. Subsequent studies have used the Cre-lox system in mice and zebrafish to create tissue specific conditional knockouts. A second transgenic line must be created, in which loxP recognition sites flank a portion of a particular critical housekeeping gene such as DNA polymerase-β. However, in some cases a particular gene of interest is turned on multiple times during development, in this scenario, it is possible to use an inducible version of the transgene, the Cre-ERt loxP approach
13.
Alkyl
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In organic chemistry, an alkyl substituent is an alkane missing one hydrogen. The term alkyl is intentionally unspecific to include many possible substitutions, an acyclic alkyl has the general formula CnH2n+1. A cycloalkyl is derived from a cycloalkane by removal of an atom from a ring and has the general formula CnH2n-1. Typically an alkyl is a part of a larger molecule, in structural formula, the symbol R is used to designate a generic alkyl group. The smallest alkyl group is methyl, with the formula CH3−, the word root alkyl is encountered in several contexts. Alkylation is an important operation in refineries, for example in the production of high-octane gasoline, alkylating antineoplastic agents refer to a class of compounds that are used to treat cancer. In such case, the alkyl is used loosely. For example, nitrogen mustards are well-known alkylating agents, but they are more complex than a mere hydrocarbon, in chemistry, alkyl refers to a group, a substituent, that is attached to other molecular fragments. For example, alkyl lithium reagents have the empirical formula Li, a dialkyl ether is an ether with two alkyl groups, e. g. diethyl ether. In medicinal chemistry, the incorporation of alkyl chains into some chemical compounds increases their lipophilicity and this strategy has been used to increase the antimicrobial activity of flavanones and chalcones. Usually alkyl groups are attached to atoms or groups of atoms. Free alkyls occur as neutral compounds, as anions, or as cations, the neutral alkyl free radicals have no special name. Such species are encountered only as transient intermediates, but some are quite stable. Typically alkyl cations are generated using super acids, alkyl anions are observed in the presence of strong bases, alkyls are commonly observed in mass spectrometry of organic compounds. The simplest series have the general formula CnH2n+1, alkyls include methyl, CH3·, ethyl, propyl, butyl, pentyl, and so on. Alkyl groups that one ring have the formula CnH2n−1, e. g. cyclopropyl and cyclohexyl. First, five atoms comprise the longest straight chain of carbon centers, the parent five-carbon compound is named pentane. The methyl substituent or group is highlighted red, according to the usual rules of nomenclature, alkyl groups are included in the name of the molecule before the root, as in methylpentane
14.
Sodium dodecyl sulfate
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Sodium dodecyl sulfate, synonymously sodium lauryl sulfate, is a synthetic organic compound with the formula CH311SO4Na. It is a surfactant used in many cleaning and hygiene products. The sodium salt is of a class of organics. It consists of a 12-carbon tail attached to a group, i. e. it is the sodium salt of dodecyl hydrogen sulfate. Its hydrocarbon tail combined with a polar headgroup give the compound amphiphilic properties, SDS is in the family of organosulfate compounds, and has the formula, CH311SO4Na, that is, it is the sodium salt of a 12-carbon alcohol that has been esterified to sulfuric acid. An alternative description is that it is a group with a pendant. As a result of its tail, and its anionic head group, it has amphiphilic properties that allow it to form micelles. The critical micelle concentration in water at 25 °C is 8.2 mM. The micelle ionization fraction is around 0.3, SDS is synthesized by treating lauryl alcohol with sulfur trioxide gas, oleum, or chlorosulfuric acid to produce hydrogen lauryl sulfate. The resulting product is then neutralized through the addition of sodium hydroxide or sodium carbonate, lauryl alcohol can be used in pure form or may be derived from either coconut or palm kernel oil by hydrolysis, followed by hydrogenation. When produced from these sources, commercial samples of these SDS products are not pure SDS. For instance, SDS is a component, along with other chain-length amphiphiles, when produced from coconut oil, SDS is available commercially in powder, pellet, and other forms, as well as in aqueous solutions of varying concentrations. SDS is mainly used in detergents for laundry with many cleaning applications and it is used as an emulsifying agent and whipping aid. SLS is reported to temporarily diminish perception of sweetness, the electrostatic repulsion that is created by SDS binding forces proteins into a rod-like shape, thereby eliminating differences in shape as a factor for electrophoretic separation in gels. SDS is used in a technique for preparing brain tissues for study by optical microscopy. Along with sodium dodecylbenzene sulfonate and Triton X-100, aqueous solutions of SDS are popular for dispersing or suspending nanotubes, in products intended for prolonged contact with skin, concentrations should not exceed 1%. Like all detergent surfactants, sodium lauryl sulfate removes oils from the skin and it has been shown to irritate the skin of the face, with prolonged and constant exposure in young adults. SDS may worsen skin problems in individuals with chronic skin hypersensitivity, in animal studies SDS appears to cause skin and eye irritation
15.
Linoleic acid
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Linoleic acid is a polyunsaturated omega-6 fatty acid. It is a liquid at room temperature. In physiological literature, it has a number of 18,2 cis. Linoleic acid is an acid with an 18-carbon chain and two cis double bonds, with the first double bond located at the sixth carbon from the methyl end. Linoleic acid belongs to one of the two families of essential fatty acids, which means that the body cannot synthesize it from other food components. The word linoleic derived from the Greek word linon, oleic means of, relating to, or derived from oil of olive or of or relating to oleic acid because saturating the omega-6 double bond produces oleic acid. LA is a fatty acid used in the biosynthesis of arachidonic acid and thus some prostaglandins, leukotrienes. It is found in the lipids of cell membranes and it is abundant in many nuts, fatty seeds and their derived vegetable oils, comprising over half of poppy seed, safflower, sunflower, corn, and soybean oils. LA is converted by various lipoxygenases, cyclooxygenases, certain cytochrome P450 enzymes, certain cytochrome P450 enzymes, the CYP epoxygenases, metabolize LA to epoxide products viz. its 12, 13-epoxide, Vernolic acid and its 9, 10-epoxide, Coronaric acid. All of these LA products have bioactivity and are implicated in human physiology and pathology as indicated in the cited linkages, linoleic acid is an essential fatty acid that must be consumed for proper health. A diet only deficient in linoleate causes mild skin scaling, hair loss, along with oleic acid, linoleic acid is released by cockroaches upon death which has the effect of preventing other roaches from entering the area. This is similar to the found in ants and bees. The first step in the metabolism of LA is performed by Δ6desaturase, there is evidence suggesting that infants lack Δ6desaturase of their own, and must acquire it through breast milk. Studies show that breast-milk fed babies have higher concentrations of GLA than formula-fed babies, GLA is converted to dihomo-gamma-linolenic acid, which in turn is converted to arachidonic acid. The three types of eicosanoids are prostaglandins, thromboxanes, and leukotrienes, eicosanoids produced from AA tend to promote inflammation and promote growth during and after physical activity in healthy humans. For example, both AA-derived thrombaxane and leukotrieneB4 are proaggregatory and vasoconstrictive eicosanoids during inflammation, there are some suggested negative health effects related to this inflammation promoting function of linoleic acid as an omega-6 fatty acid. Linoleic acid is used in making quick-drying oils, which are useful in oil paints and these applications exploit the easy reaction of the linoleic acid with oxygen in air, which leads to crosslinking and formation of a stable film called linoxyn. Reduction of linoleic acid yields linoleyl alcohol, linoleic acid is a surfactant with a critical micelle concentration of 1.5 x 10−4 M @ pH7.5
16.
Oleic acid
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Oleic acid is a fatty acid that occurs naturally in various animal and vegetable fats and oils. It is an odorless, colorless oil, although commercial samples may be yellowish, in chemical terms, oleic acid is classified as a monounsaturated omega-9 fatty acid, abbreviated with a lipid number of 18,1 cis-9. The term oleic means related to, or derived from, olive oil which is composed of oleic acid. The corresponding stereoisomer trans-9-Octadecenoic acid is called Elaidic acid and these isomers have distinct physical properties and biochemical properties. Elaidic acid, the most abundant trans fatty acid in diet, fatty acids do not often occur as such in biological systems. Instead fatty acids oleic acid occur as their esters, commonly triglycerides. Fatty acids can be obtained via the process of saponification, triglycerides of oleic acid compose the majority of olive oil, although there may be less than 2. 0% as free acid in virgin olive oil, with higher concentrations making the olive oil inedible. It is abundantly present in animal fats, constituting 37 to 56% of chicken. Oleic acid is the most abundant fatty acid in adipose tissue. Oleic acid is emitted by the corpses of a number of insects, including bees and Pogonomyrmex ants. If a live bee or ant is daubed with oleic acid, the oleic acid smell also may indicate danger to living insects, prompting them to avoid others who have succumbed to disease or places where predators lurk. The biosynthesis of oleic acid involves the action of the enzyme stearoyl-CoA 9-desaturase acting on stearoyl-CoA, in effect, stearic acid is dehydrogenated to give the monounsaturated derivative oleic acid. Oleic acid undergoes the reactions of acids and alkenes. It is soluble in aqueous base to give soaps called oleates, iodine adds across the double bond. Hydrogenation of the double bond yields the saturated derivative stearic acid, oxidation at the double bond occurs slowly in air, and is known as rancidification in foodstuffs or drying in coatings. Reduction of the acid group yields oleyl alcohol. Ozonolysis of oleic acid is an important route to azelaic acid, the coproduct is nonanoic acid, H17C8CH=CHC7H14CO2H + 4O → H17C8CO2H + HO2CC7H14CO2H Esters of azelaic acid find applications in lubrication and plasticizers. The trans isomer of oleic acid is called elaidic acid, a naturally occurring isomer of oleic acid is petroselinic acid
17.
Rhodamine
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Rhodamine /ˈroʊdəmiːn/ is a family of related chemical compounds, fluorone dyes. Examples are Rhodamine 6G and Rhodamine B and they are used as dyes and as dye laser gain media. They are often used as a tracer dye within water to determine the rate and direction of flow, Rhodamine dyes fluoresce and can thus be detected easily and inexpensively with instruments called fluorometers. Rhodamine dyes are used extensively in biotechnology applications such as microscopy, flow cytometry, fluorescence correlation spectroscopy. Rhodamine dyes are generally toxic, and are soluble in water, the laser dye rhodamine 123 is also used in biochemistry to inhibit mitochondrion function. Rhodamine 123 seems to bind to the membranes and inhibit transport processes, especially the electron transport chain. It is a substrate of P-glycoprotein, which is overexpressed in cancer cells. Recent reports indicate that rhodamine 123 may be also a substrate of multidrug resistance-associated protein, or more specifically, TRITC is the base rhodamine molecule functionalized with an isothiocyanate group, replacing a hydrogen atom on the bottom ring of the structure. This derivative is reactive towards amine groups on proteins inside cells, a succinimidyl-ester functional group attached to the rhodamine core, creating NHS-rhodamine, forms another common amine-reactive derivative
18.
International Standard Serial Number
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An International Standard Serial Number is an eight-digit serial number used to uniquely identify a serial publication. The ISSN is especially helpful in distinguishing between serials with the same title, ISSN are used in ordering, cataloging, interlibrary loans, and other practices in connection with serial literature. The ISSN system was first drafted as an International Organization for Standardization international standard in 1971, ISO subcommittee TC 46/SC9 is responsible for maintaining the standard. When a serial with the content is published in more than one media type. For example, many serials are published both in print and electronic media, the ISSN system refers to these types as print ISSN and electronic ISSN, respectively. The format of the ISSN is an eight digit code, divided by a hyphen into two four-digit numbers, as an integer number, it can be represented by the first seven digits. The last code digit, which may be 0-9 or an X, is a check digit. Formally, the form of the ISSN code can be expressed as follows, NNNN-NNNC where N is in the set, a digit character. The ISSN of the journal Hearing Research, for example, is 0378-5955, where the final 5 is the check digit, for calculations, an upper case X in the check digit position indicates a check digit of 10. To confirm the check digit, calculate the sum of all eight digits of the ISSN multiplied by its position in the number, the modulus 11 of the sum must be 0. There is an online ISSN checker that can validate an ISSN, ISSN codes are assigned by a network of ISSN National Centres, usually located at national libraries and coordinated by the ISSN International Centre based in Paris. The International Centre is an organization created in 1974 through an agreement between UNESCO and the French government. The International Centre maintains a database of all ISSNs assigned worldwide, at the end of 2016, the ISSN Register contained records for 1,943,572 items. ISSN and ISBN codes are similar in concept, where ISBNs are assigned to individual books, an ISBN might be assigned for particular issues of a serial, in addition to the ISSN code for the serial as a whole. An ISSN, unlike the ISBN code, is an identifier associated with a serial title. For this reason a new ISSN is assigned to a serial each time it undergoes a major title change, separate ISSNs are needed for serials in different media. Thus, the print and electronic versions of a serial need separate ISSNs. Also, a CD-ROM version and a web version of a serial require different ISSNs since two different media are involved, however, the same ISSN can be used for different file formats of the same online serial
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PubMed Identifier
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PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval, from 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home-, the PubMed system was offered free to the public in June 1997, when MEDLINE searches via the Web were demonstrated, in a ceremony, by Vice President Al Gore. Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog. As of 5 January 2017, PubMed has more than 26.8 million records going back to 1966, selectively to the year 1865, and very selectively to 1809, about 500,000 new records are added each year. As of the date,13.1 million of PubMeds records are listed with their abstracts. In 2016, NLM changed the system so that publishers will be able to directly correct typos. Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMeds search window, when a journal article is indexed, numerous article parameters are extracted and stored as structured information. Such parameters are, Article Type, Secondary identifiers, Language, publication type parameter enables many special features. As these clinical girish can generate small sets of robust studies with considerable precision, since July 2005, the MEDLINE article indexing process extracts important identifiers from the article abstract and puts those in a field called Secondary Identifier. The secondary identifier field is to store numbers to various databases of molecular sequence data, gene expression or chemical compounds. For clinical trials, PubMed extracts trial IDs for the two largest trial registries, ClinicalTrials. gov and the International Standard Randomized Controlled Trial Number Register, a reference which is judged particularly relevant can be marked and related articles can be identified. If relevant, several studies can be selected and related articles to all of them can be generated using the Find related data option, the related articles are then listed in order of relatedness. To create these lists of related articles, PubMed compares words from the title and abstract of each citation, as well as the MeSH headings assigned, using a powerful word-weighted algorithm. The related articles function has been judged to be so precise that some researchers suggest it can be used instead of a full search, a strong feature of PubMed is its ability to automatically link to MeSH terms and subheadings. Examples would be, bad breath links to halitosis, heart attack to myocardial infarction, where appropriate, these MeSH terms are automatically expanded, that is, include more specific terms. Terms like nursing are automatically linked to Nursing or Nursing and this important feature makes PubMed searches automatically more sensitive and avoids false-negative hits by compensating for the diversity of medical terminology. The My NCBI area can be accessed from any computer with web-access, an earlier version of My NCBI was called PubMed Cubby
20.
International Standard Book Number
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The International Standard Book Number is a unique numeric commercial book identifier. An ISBN is assigned to each edition and variation of a book, for example, an e-book, a paperback and a hardcover edition of the same book would each have a different ISBN. The ISBN is 13 digits long if assigned on or after 1 January 2007, the method of assigning an ISBN is nation-based and varies from country to country, often depending on how large the publishing industry is within a country. The initial ISBN configuration of recognition was generated in 1967 based upon the 9-digit Standard Book Numbering created in 1966, the 10-digit ISBN format was developed by the International Organization for Standardization and was published in 1970 as international standard ISO2108. Occasionally, a book may appear without a printed ISBN if it is printed privately or the author does not follow the usual ISBN procedure, however, this can be rectified later. Another identifier, the International Standard Serial Number, identifies periodical publications such as magazines, the ISBN configuration of recognition was generated in 1967 in the United Kingdom by David Whitaker and in 1968 in the US by Emery Koltay. The 10-digit ISBN format was developed by the International Organization for Standardization and was published in 1970 as international standard ISO2108, the United Kingdom continued to use the 9-digit SBN code until 1974. The ISO on-line facility only refers back to 1978, an SBN may be converted to an ISBN by prefixing the digit 0. For example, the edition of Mr. J. G. Reeder Returns, published by Hodder in 1965, has SBN340013818 -340 indicating the publisher,01381 their serial number. This can be converted to ISBN 0-340-01381-8, the check digit does not need to be re-calculated, since 1 January 2007, ISBNs have contained 13 digits, a format that is compatible with Bookland European Article Number EAN-13s. An ISBN is assigned to each edition and variation of a book, for example, an ebook, a paperback, and a hardcover edition of the same book would each have a different ISBN. The ISBN is 13 digits long if assigned on or after 1 January 2007, a 13-digit ISBN can be separated into its parts, and when this is done it is customary to separate the parts with hyphens or spaces. Separating the parts of a 10-digit ISBN is also done with either hyphens or spaces, figuring out how to correctly separate a given ISBN number is complicated, because most of the parts do not use a fixed number of digits. ISBN issuance is country-specific, in that ISBNs are issued by the ISBN registration agency that is responsible for country or territory regardless of the publication language. Some ISBN registration agencies are based in national libraries or within ministries of culture, in other cases, the ISBN registration service is provided by organisations such as bibliographic data providers that are not government funded. In Canada, ISBNs are issued at no cost with the purpose of encouraging Canadian culture. In the United Kingdom, United States, and some countries, where the service is provided by non-government-funded organisations. Australia, ISBNs are issued by the library services agency Thorpe-Bowker
. PMID 27597115.