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.
Phenols
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In organic chemistry, phenols, sometimes called phenolics, are a class of chemical compounds consisting of a hydroxyl group bonded directly to an aromatic hydrocarbon group. The simplest of the class is phenol, which is also called carbolic acid C 6H 5OH, phenolic compounds are classified as simple phenols or polyphenols based on the number of phenol units in the molecule. Synonyms are arenols or aryl alcohols, phenolic compounds are synthesized industrially, they also are produced by plants and microorganisms, with variation between and within species. Although similar to alcohols, phenols have unique properties and are not classified as alcohols and they have higher acidities due to the aromatic rings tight coupling with the oxygen and a relatively loose bond between the oxygen and hydrogen. The acidity of the group in phenols is commonly intermediate between that of aliphatic alcohols and carboxylic acids. Phenols can have two or more hydroxy groups bonded to the ring in the same molecule. The simplest examples are the three benzenediols, each having two groups on a benzene ring. Organisms that synthesize phenolic compounds do so in response to pressures such as pathogen and insect attack, UV radiation. As they are present in food consumed in human diets and in used in traditional medicine of several cultures, their role in human health. Some phenols are germicidal and are used in formulating disinfectants, others possess estrogenic or endocrine disrupting activity. They can also be classified on the basis of their number of phenol groups and they can therefore be called simple phenols or monophenols, with only one phenolic group, or di-, tri- and oligophenols, with two, three or several phenolic groups respectively. The phenolic unit can be found dimerized or further polymerized, creating a new class of polyphenol, two natural phenols from two different categories, for instance a flavonoid and a lignan, can combine to form a hybrid class like the flavonolignans. Nomenclature of polymers, Plants in the genus Humulus and Cannabis produce terpenophenolic metabolites, phenolic lipids are long aliphatic chains bonded to a phenolic moiety. The majority of compounds are solubles molecules but the smaller molecules can be volatiles. Many natural phenols present chirality within their molecule, an example of such molecules is catechin. Cavicularin is an unusual macrocycle because it was the first compound isolated from nature displaying optical activity due to the presence of planar chirality, natural phenols chemically interact with many other substances. Stacking, a property of molecules with aromaticity, is seen occurring between phenolic molecules. When studied in mass spectrometry, phenols easily form adduct ions with halogens and they can also interact with the food matrices or with different forms of silica
3.
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
4.
Gallic acid
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Gallic acid is a trihydroxybenzoic acid, a type of phenolic acid, found in gallnuts, sumac, witch hazel, tea leaves, oak bark, and other plants. The chemical formula of gallic acid is C6H23COOH and it is found both free and as part of hydrolyzable tannins. The gallic acid groups are bonded to form dimers such as ellagic acid. Hydrolyzable tannins break down on hydrolysis to give gallic acid and glucose or ellagic acid and glucose, known as gallotannins and ellagitannins, gallic acid forms intermolecular esters such as digallic and trigallic acids, and cyclic ether-esters. Gallic acid can also be used as a material in the synthesis of the psychedelic alkaloid mescaline. The name is derived from oak galls, which were used to prepare tannic acid. Despite the name, gallic acid does not contain gallium, salts and esters of gallic acid are termed gallates. Pliny the Elder describes his experiments with it and writes that it was used to produce dyes, galls from oak trees were crushed and mixed with water, producing tannic acid. Gallic acid was one of the used by Angelo Mai, among other early investigators of palimpsests, to clear the top layer of text off. Mai was the first to employ it, but did so with a heavy hand, gallic acid was first studied by the Swedish chemist Carl Wilhelm Scheele in 1786. Gallic acid is a component of some pyrotechnic whistle mixtures, gallic acid is formed from 3-dehydroshikimate by the action of the enzyme shikimate dehydrogenase to produce 3, 5-didehydroshikimate. This latter compound tautomerizes to form the redox equivalent gallic acid, gallate dioxygenase is an enzyme found in Pseudomonas putida that catalyses the reaction gallate + O2 → -4-oxobut-1-ene-1,2, 4-tricarboxylate. Gallate decarboxylase is another enzyme in the degradation of gallic acid, gallate 1-beta-glucosyltransferase is an enzyme that uses UDP-glucose and gallate, whereas its two products are UDP and 1-galloyl-beta-D-glucose. It is a carbonic anhydrase inhibitor. In basic research, gallic acid extracted from seeds has been shown to inhibit the formation of amyloid fibrils, one of the potential causes of Alzheimers disease. One study indicated that gallic acid has this effect on amyloid protein formation by modifying the properties of alpha-synuclein, gallic acid is classified as a mutagen and a teratogen. Gallic acid is found in a number of plants, such as the parasitic plant Cynomorium coccineum, the aquatic plant Myriophyllum spicatum. Gallic acid is found in various oak species, Caesalpinia mimosoides
5.
Pyrogallol
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Pyrogallol is an organic compound with the formula C6H33. It is a white solid although samples are typically brownish because of its sensitivity toward oxygen and it is one of three isomeric benzenetriols. It is produced in the manner it was first prepared by Scheele, presently gallic acid is obtained from tannin. Heating induces decarboxylation, Because tannin is expensive, many routes have been devised. An alternate preparation involves treating para-chlorophenoldisulphonic acid with potassium hydroxide, a variant on the route to phenols from sulfonic acids. The aquatic plant Myriophyllum spicatum produces pyrogallic acid, when in alkaline solution, it absorbs oxygen from the air, turning brown from a colourless solution. It can be used in this way to calculate the amount of oxygen in air, one can find its uses in hair dying, dying of suturing materials and for oxygen absorption in gas analysis. Pyrogallol was also used as an agent in black-and-white developers. In those days it had a reputation for erratic and unreliable behavior and it experienced a revival starting in the 1980s due largely to the efforts of experimenters Gordon Hutchings and John Wimberley. Hutchings spent over a decade working on formulas, eventually producing one he named PMK. From 1969 to 1977, Wimberley experimented with the Pyrogallol developing agent and he published his formula for WD2D in 1977 in Petersons Photographic. PMK and other modern pyro formulations are now used by many black-and-white photographers, the Film Developing Cookbook has examples. Pyrogallol use, e. g. in hair dye formulations, is declining because of concerns about its toxicity
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.
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
8.
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
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