1.
Pistacia lentiscus
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Pistacia lentiscus is a dioecious evergreen shrub or small tree of the pistacio genus growing up to 4 m tall which is cultivated for its aromatic resin, mainly on the Greek island of Chios. It resists heavy frosts and grows on all types of soils and it is also found in woodlands, dehesas, Kermes oak wood, oaks wood, garrigue, maquis, hills, gorges, canyons, and rocky hillsides of the entire Mediterranean area. It is a hardy pioneer species dispersed by birds. When older, it develops some large trunks and numerous thicker and longer branches, in appropriate areas, when allowed to grow freely and age, it often becomes a tree of up to 7 m. However, logging, grazing, and fires often prevent its development, the leaves are alternate, leathery, and compound paripinnate with five or six pairs of deep-green leaflets. It presents very small flowers, the male with five stamens, the fruit is a drupe, first red and then black when ripe, about 4 mm in diameter. In tourist areas, with palmitos or Mediterranean dwarf palm, and exotic plants, it is chosen to repopulate gardens and resorts, because of its strength. Unlike other species of Pistacia, it retains its leaves throughout the year, a related species, P. saportae, has been shown by DNA analysis to be a hybrid between maternal P. lentiscus and paternal P. terebinthus. The hybrid has imparipinnate leaves, with leaflets semipersistent, subsessile terminal, Pistacia lentiscus is native throughout the Mediterranean region, from Morocco and Iberian peninsula in the west through southern France and Turkey to Iraq and Iran in the east. It is also native to the Canary Islands, the word mastic derives from the Latin word Masticare, in Greek, μαστιχάω verb mastichein or massein. Within the European Union, mastic production in Chios is granted protected designation of origin, although the tree is native to all of the Mediterranean region, only on southern Chios is the mastic trees bark scored to weep the masticha resin. The islands mastic production is controlled by a co-operative of medieval villages, collectively known as the Mastichochoria, originally liquid, it is hardened, when the weather turns cold, into drops or patties of hard, brittle, translucent resin. When chewed, the resin softens and becomes a bright white, the resin is collected by bleeding the trees from small cuts made in the bark of the main branches, and allowing the sap to drip onto the specially prepared ground below. The harvesting is done during the summer between June and September, after the mastic is collected, it is washed manually and is set aside to dry, away from the sun, as it will start melting again. Mastic resin is a relatively expensive kind of spice, it has been used principally as a chewing gum for at least 2,400 years, the flavour can be described as a strong, slightly smoky, resiny aroma and can be an acquired taste. Some scholars identify the bakha בכא mentioned in the Bible—as in the Valley of Baca of Psalm 84—with the mastic plant, the Valley of Baca is thought to be a valley near Jerusalem that was covered with low mastic shrubbery, much like some hillsides in northern Israel today. Mastic is known to have been popular in Roman times when children chewed it and it was the Sultans privilege to chew mastic, and it was considered to have healing properties. The spices use was widened when Chios became part of the Ottoman Empire, and it remains popular in North Africa, the Mastichochoria are located in the southern part of Chios
2.
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
3.
European Chemicals Agency
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ECHA is the driving force among regulatory authorities in implementing the EUs chemicals legislation. ECHA helps companies to comply with the legislation, advances the safe use of chemicals, provides information on chemicals and it is located in Helsinki, Finland. The Agency, headed by Executive Director Geert Dancet, started working on 1 June 2007, the REACH Regulation requires companies to provide information on the hazards, risks and safe use of chemical substances that they manufacture or import. Companies register this information with ECHA and it is freely available on their website. So far, thousands of the most hazardous and the most commonly used substances have been registered, the information is technical but gives detail on the impact of each chemical on people and the environment. This also gives European consumers the right to ask whether the goods they buy contain dangerous substances. The Classification, Labelling and Packaging Regulation introduces a globally harmonised system for classifying and labelling chemicals into the EU. This worldwide system makes it easier for workers and consumers to know the effects of chemicals, companies need to notify ECHA of the classification and labelling of their chemicals. So far, ECHA has received over 5 million notifications for more than 100000 substances, the information is freely available on their website. Consumers can check chemicals in the products they use, Biocidal products include, for example, insect repellents and disinfectants used in hospitals. The Biocidal Products Regulation ensures that there is information about these products so that consumers can use them safely. ECHA is responsible for implementing the regulation, the law on Prior Informed Consent sets guidelines for the export and import of hazardous chemicals. Through this mechanism, countries due to hazardous chemicals are informed in advance and have the possibility of rejecting their import. Substances that may have effects on human health and the environment are identified as Substances of Very High Concern 1. These are mainly substances which cause cancer, mutation or are toxic to reproduction as well as substances which persist in the body or the environment, other substances considered as SVHCs include, for example, endocrine disrupting chemicals. Companies manufacturing or importing articles containing these substances in a concentration above 0 and they are required to inform users about the presence of the substance and therefore how to use it safely. Consumers have the right to ask the retailer whether these substances are present in the products they buy, once a substance has been officially identified in the EU as being of very high concern, it will be added to a list. This list is available on ECHA’s website and shows consumers and industry which chemicals are identified as SVHCs, Substances placed on the Candidate List can then move to another list
4.
Tannic acid
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Tannic acid is a specific form of tannin, a type of polyphenol. Its weak acidity is due to the numerous groups in the structure. Commercial tannic acid is extracted from any of the following plant part, Tara pods. Sometimes extracts from chestnut or oak wood are also described as tannic acid and it is a yellow to light brown amorphous powder,2850 grams dissolves in one litre of water. While tannic acid is a type of tannin, the two terms are sometimes used interchangeably. The long-standing misuse of the terms, and its inclusion in scholarly articles has compounded the confusion and this is particularly widespread in relation to green tea and black tea, both of which contain tannin but not tannic acid. Tannic acid is not a standard for any type of tannin analysis because of its poorly defined composition. Quercitannic acid is one of the two forms of acid found in oak bark and leaves. The other form is called gallotannic acid and is found in oak galls, the quercitannic acid molecule is also present in quercitron, a yellow dye obtained from the bark of the Eastern black oak, a forest tree indigenous in North America. It is described as a yellowish brown amorphous substance, in 1838, Jöns Jacob Berzelius wrote that quercitannate is used to dissolve morphine. In 1865 in the volume of A dictionary of chemistry, Henry Watts wrote. It differs however from the latter in not being convertible into gallic acid and it is precipitated by sulfuric acid in red flocks. According to Rochleder, the acid of black tea is the same as that of oak-bark. In 1880, Etti gave for it the molecular formula C17H16O9 and he described it as an unstable substance, having a tendency to give off water to form anhydrides, one of which is called oak-red. For him, it was not a glycoside, in Allen’s Commercial Organic Analysis, published in 1912, the formula given was C19H16O10. Other authors gave other molecular formulas like C28H26O15, while another formula found is C28H24O11, according to Lowe, two forms of the principle exist – one soluble in water, of the formula C28H28O14, and the other scarcely soluble, C28H24O12. Both are changed by the loss of water into oak red, quercitannic acid was for a time a standard used to assess the phenolic content in spices, given as quercitannic acid equivalent. In an interesting note, the inventor Edward G. Acheson discovered that gallotannic acid greatly improved the plasticity of clay
5.
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
6.
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
7.
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
8.
ChEMBL
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ChEMBL or ChEMBLdb is a manually curated chemical database of bioactive molecules with drug-like properties. It is maintained by the European Bioinformatics Institute, of the European Molecular Biology Laboratory, based at the Wellcome Trust Genome Campus, Hinxton, the database, originally known as StARlite, was developed by a biotechnology company called Inpharmatica Ltd. later acquired by Galapagos NV. The data was acquired for EMBL in 2008 with an award from The Wellcome Trust, resulting in the creation of the ChEMBL chemogenomics group at EMBL-EBI, the ChEMBL database contains compound bioactivity data against drug targets. Bioactivity is reported in Ki, Kd, IC50, and EC50, data can be filtered and analyzed to develop compound screening libraries for lead identification during drug discovery. ChEMBL version 2 was launched in January 2010, including 2.4 million bioassay measurements covering 622,824 compounds and this was obtained from curating over 34,000 publications across twelve medicinal chemistry journals. ChEMBLs coverage of available bioactivity data has grown to become the most comprehensive ever seen in a public database, in October 2010 ChEMBL version 8 was launched, with over 2.97 million bioassay measurements covering 636,269 compounds. ChEMBL_10 saw the addition of the PubChem confirmatory assays, in order to integrate data that is comparable to the type, ChEMBLdb can be accessed via a web interface or downloaded by File Transfer Protocol. It is formatted in a manner amenable to computerized data mining, ChEMBL is also integrated into other large-scale chemistry resources, including PubChem and the ChemSpider system of the Royal Society of Chemistry. In addition to the database, the ChEMBL group have developed tools and these include Kinase SARfari, an integrated chemogenomics workbench focussed on kinases. The system incorporates and links sequence, structure, compounds and screening data, the primary purpose of ChEMBL-NTD is to provide a freely accessible and permanent archive and distribution centre for deposited data. July 2012 saw the release of a new data service, sponsored by the Medicines for Malaria Venture. The data in this service includes compounds from the Malaria Box screening set, myChEMBL, the ChEMBL virtual machine, was released in October 2013 to allow users to access a complete and free, easy-to-install cheminformatics infrastructure. In December 2013, the operations of the SureChem patent informatics database were transferred to EMBL-EBI, in a portmanteau, SureChem was renamed SureChEMBL. 2014 saw the introduction of the new resource ADME SARfari - a tool for predicting and comparing cross-species ADME targets
9.
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
10.
Depside
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A depside is a type of polyphenolic compound composed of two or more monocyclic aromatic units linked by an ester bond. Depsides are most often found in lichens, but have also been isolated from higher plants, depsides have antibiotic, anti-HIV, antioxidant, and anti-proliferative activity. As inhibitors of synthesis and leukotriene B4 biosynthesis, depsides are potent non-steroidal anti-inflammatories. A depsidase is a type of enzyme that cuts depside bonds, gyrophoric acid, found in the lichen Cryptothecia rubrocincta, is a depside. Salsalate homodimer formed from self-condensation of salicylic acid to form ester linkage
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