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.
Isomer
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An isomer is a molecule with the same molecular formula as another molecule, but with a different chemical structure. That is, isomers contain the number of atoms of each element. Isomers do not necessarily share similar properties, unless they also have the functional groups. There are two forms of isomerism, structural isomerism and stereoisomerism. In structural isomers, sometimes referred to as constitutional isomers, the atoms, Structural isomers have different IUPAC names and may or may not belong to the same functional group. For example, two position isomers would be 2-fluoropropane and 1-fluoropropane, illustrated on the side of the diagram above. In skeletal isomers the main chain is different between the two isomers. This type of isomerism is most identifiable in secondary and tertiary alcohol isomers, tautomers are structural isomers that spontaneously interconvert with each other, even when pure. They have different chemical properties and, as a consequence, distinct reactions characteristic to each form are observed, if the interconversion reaction is fast enough, tautomers cannot be isolated from each other. An example is when they differ by the position of a proton, such as in keto/enol tautomerism, there is, however, another isomer of C3H8O that has significantly different properties, methoxyethane. Unlike the isomers of propanol, methoxyethane has an oxygen connected to two carbons rather than to one carbon and one hydrogen. Methoxyethane is an ether, not an alcohol, because it lacks a hydroxyl group, propadiene and propyne are examples of isomers containing different bond types. Propadiene contains two double bonds, whereas propyne contains one triple bond, in stereoisomers the bond structure is the same, but the geometrical positioning of atoms and functional groups in space differs. This class includes enantiomers which are non-superposable mirror-images of each other, and diastereomers, enantiomers always contain chiral centers and diastereomers often do, but there are some diastereomers that neither are chiral nor contain chiral centers. Another type of isomer, conformational isomers, may be rotamers, diastereomers, for example, ortho- position-locked biphenyl systems have enantiomers. E/Z isomers, which have restricted rotation at a bond, are configurational isomers. They are classified as diastereomers, whether or not they contain any chiral centers, e/Z notation depicts absolute stereochemistry, which is an unambiguous descriptor based on CIP priorities. Cis–trans isomers are used to describe any molecules with restricted rotation in the molecule, for molecules with C=C double bonds, these descriptors describe relative stereochemistry only based on group bulkiness or principal carbon chain, and so can be ambiguous
8.
Caffeic acid
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Caffeic acid is an organic compound that is classified as a hydroxycinnamic acid. This yellow solid consists of both phenolic and acrylic functional groups and it is found in all plants because it is a key intermediate in the biosynthesis of lignin, one of the principal components of plant biomass and its residues. Caffeic acid can be found in the bark of Eucalyptus globulus and it can also be found in the freshwater fern Salvinia molesta or in the mushroom Phellinus linteus. Caffeic acid is found at a very modest level in coffee and it is one of the main natural phenols in argan oil. It is at a high level in black chokeberry and in fairly high level in lingonberry. It is also high in the South American herb yerba mate. It is also found in grain, and in rye grain. Caffeic acid, which is unrelated to caffeine, is biosynthesized by hydroxylation of coumaroyl ester of quinic acid and this hydroxylation produces the caffeic acid ester of shikimic acid, which converts to chlorogenic acid. It is the precursor to acid, coniferyl alcohol, and sinapyl alcohol. The transformation to ferulic acid is catalyzed by the enzyme caffeate O-methyltransferase, caffeic acid and its derivative caffeic acid phenethyl ester are produced in many kinds of plants. Dihydroxyphenylalanine ammonia-lyase was presumed to use 3, 4-dihydroxy-L-phenylalanine to produce trans-caffeate, however, the EC number for this purported enzyme was deleted in 2007, as no evidence has emerged for its existence. Caffeate O-methyltransferase is a responsible for the transformation of caffeic acid into ferulic acid. Caffeic acid and related o-diphenols are rapidly oxidized by o-diphenol oxidases in tissue extracts, caffeate 3, 4-dioxygenase is an enzyme that uses caffeic acid and oxygen to produce 3--cis, cis-muconate. 3-O-caffeoylshikimic acid and its isomers, are enzymic browning substrates found in dates, caffeic acid is an antioxidant in vitro and also in vivo. Caffeic acid also shows immunomodulatory and anti-inflammatory activity, caffeic acid outperformed the other antioxidants, reducing aflatoxin production by more than 95 percent. The studies are the first to show that stress that would otherwise trigger or enhance Aspergillus flavus aflatoxin production can be stymied by caffeic acid. This opens the door to use as a natural fungicide by supplementing trees with antioxidants, studies of the carcinogenicity of caffeic acid have mixed results. Some studies have shown that it inhibits carcinogenesis, and other experiments show carcinogenic effects, oral administration of high doses of caffeic acid in rats has caused stomach papillomas
9.
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
10.
Cinnamic acid
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Cinnamic acid is an organic compound with the formula C6H5CHCHCO2H. It is a crystalline compound that is slightly soluble in water. Classified as a carboxylic acid, it occurs naturally in a number of plants. It exists as both a cis and an isomer, although the latter is more common. It is obtained from oil of cinnamon, or from such as storax. It is also found in shea butter, Cinnamic acid has a honey-like odor, it and its more volatile ethyl ester are flavor components in the essential oil of cinnamon, in which related cinnamaldehyde is the major constituent. Cinnamic acid is part of the biosynthetic shikimate and phenylpropanoid pathways. Its biosynthesis is performed by action of the enzyme phenylalanine ammonia-lyase on phenylalanine, the original synthesis of cinnamic acid involves the Perkin reaction, which entails the base-catalysed condensation of acetic anhydride and benzaldehyde. Rainer Ludwig Claisen described the synthesis of esters by the reaction of benzaldehyde. The reaction is known as the Aldol condensation and it can also be prepared from cinnamaldehyde and benzal chloride. Another way of preparing Cinnamic acid is by the Knövenaegel–Hans condensation reaction, the reactants for this are the corresponding benzaldehyde and malonic acid in the presence of a weak base, followed by acid hydrolysis. Cinnamic acid is used in flavors, synthetic indigo, and certain pharmaceuticals, a major use is in the manufacturing of the methyl, ethyl, and benzyl esters for the perfume industry. Cinnamic acid is a precursor to the sweetener aspartame via enzyme-catalysed amination to phenylalanine, Cinnamic acid can dimerize in non-polar solvents resulting in different linear free energy relationships
11.
P-Coumaric acid
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P-Coumaric acid is a hydroxycinnamic acid, an organic compound that is a hydroxy derivative of cinnamic acid. There are three isomers of coumaric acid—o-coumaric acid, m-coumaric acid, and p-coumaric acid—that differ by the position of the substitution of the phenyl group. P-Coumaric acid is the most abundant isomer of the three in nature, p-Coumaric acid exists in two forms trans-p-coumaric acid and cis-p-coumaric acid. It is a solid that is slightly soluble in water. Together with sinapyl alcohol and coniferyl alcohols, p-coumaric acid is a component of lignin. P-Coumaric acid can be found in Gnetum cleistostachyum, p-Coumaric acid can be found in a wide variety of edible plants such as peanuts, navy beans, tomatoes, carrots, basil and garlic. It is found in wine and vinegar and it is also found in barley grain. P-Coumaric acid from pollen is a constituent of honey, p-Coumaric acid glucoside can also be found in commercial breads containing flaxseed. Diesters of p-coumaric acid can be found in carnauba wax and it is biosynthesized from cinnamic acid by the action of the P450-dependent enzyme 4-cinnamic acid hydroxylase. → C4 H It is also produced from L-tyrosine by the action of tyrosine ammonia lyase, → T A L + Ammonia + H+ p-Coumaric acid is the precursor of 4-ethylphenol produced by the yeast Brettanomyces in wine. The yeast converts this to 4-vinylphenol via the enzyme cinnamate decarboxylase, 4-Vinylphenol is further reduced to 4-ethylphenol by the enzyme vinyl phenol reductase. Coumaric acid is added to microbiological media, enabling the positive identification of Brettanomyces by smell. Cis-p-coumarate glucosyltransferase is an enzyme that uses UDP-glucose and cis-p-coumarate to produce 4-O-beta-D-glucosyl-cis-p-coumarate and this enzyme belongs to the family of glycosyltransferases, specifically the hexosyltransferases. Phloretic acid is found in the rumen of sheep fed with dried grass and is produced by hydrogenation of the 2-propenoic side chain of p-coumaric acid, p-Coumaric acid has antioxidant properties and is believed to reduce the risk of stomach cancer by reducing the formation of carcinogenic nitrosamines. This absence has been suggested as a contributor to Colony Collapse Disorder of honey bees because p-coumaric acid has been found to help honey bees detoxify certain pesticides. However, recent research has pointed to insecticides as the reason for bee deaths. Coumarin Coumaroyl-Coenzyme A Ferulic acid Cinnamic acid Phenolic content in wine p-Coumaroylated anthocyanins
12.
O-Coumaric acid
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O-Coumaric acid is a hydroxycinnamic acid, an organic compound that is a hydroxy derivative of cinnamic acid. There are three isomers of coumaric acids - o-coumaric acid, m-coumaric acid, and p-coumaric acid- that differ by the position of the substitution of the phenyl group. O-Coumaric acid can be found in vinegar, 2-coumarate reductase is an enzyme that produces 2-coumarate from 3-propanoate and NAD+. This enzyme participates in phenylalanine metabolism
13.
Umbellic acid
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Umbellic acid is a hydroxycinnamic acid. It is an isomer of caffeic acid and it is a precursor in the umbelliferone biosynthesis pathway. Umbelliferone is a phenylpropanoid and as such is synthesized from L-phenylalanine, phenylalanine is lysated into cinnamic acid, followed by hydroxylation by cinnamate 4-hydroxylase to yield 4-coumaric acid. Finally an intramolecular attack from the group of C2 to the carboxylic acid group closes the ring. The dictionary definition of acid at Wiktionary
14.
Ferulic acid
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Ferulic acid is a hydroxycinnamic acid, a type of organic compound. It is an abundant phenolic phytochemical found in plant cell wall such as arabinoxylans as covalent side chains. It is related to trans-cinnamic acid, as a component of lignin, ferulic acid is a precursor in the manufacture of other aromatic compounds. The etymology is from the genus Ferula, referring to the giant fennel, as a building block of lignocelluloses, such as pectin and lignin, ferulic acid is ubiquitous in the plant kingdom. Ferulic acid is found in the seeds of coffee, apple, artichoke, peanut, often in the form of chlorogenic acid. In cereals, ferulic acid is localized in the bran the hard layer of grain. In wheat, phenolic compounds are found in the form of insoluble bound ferulic acid. The highest known concentration of ferulic acid glucoside has been found in flax seed and it is also found in barley grain. Asterid Eudicot plants can also produce ferulic acid, the tea brewed from the leaves of yacón, a plant traditionally grown in the Northern and Central Andes, contains quantities of ferulic acid. In legumes, the white bean variety navy bean is the richest source of ferulic acid among the common bean varieties and it is also found in horse grams. In wheat grain, ferulic acid is bound to cell wall polysaccharides. Ferulic acid has been identified in Chinese medicine herbs such as Angelica sinensis, Cimicifuga heracleifolia and Lignsticum chuangxiong. It is also found in the tea brewed from the European centaury, as plant sterol esters, this compound is naturally found in rice bran oil, a popular cooking oil in several Asian countries. Ferulic acid glucoside can be found in commercial breads containing flaxseed, rye bread contains ferulic acid dehydrodimers. Biosynthesis of ferulic acid is by the action of the enzyme caffeate O-methyltransferase and it is biosynthesized from caffeic acid. Ferulic acid, together with dihydroferulic acid, is a component of lignocellulose, serving to crosslink the lignin and polysaccharides and it is an intermediate in the synthesis of monolignols, i. e. the monomers of lignin, and is also used for the synthesis of lignans. Saccharomyces cerevisiae and Pseudomonas fluorescens are also able to convert trans-ferulic acid into 2-methoxy-4-vinylphenol, in P. fluorescens, a ferulic acid decarboxylase has been isolated. Ferulic acid is one of the plant compounds that initiate Agrobacterium tumefaciens to infect plant cells
15.
5-Hydroxyferulic acid
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5-Hydroxyferulic acid is a hydroxycinnamic acid. It is a precursor in the biosynthesis of sinapic acid, phenylalanine is first converted to cinnamic acid by the action of the enzyme phenylalanine ammonia-lyase. A series of hydroxylations and methylations leads to coumaric acid, caffeic acid, ferulic acid, 5-hydroxyferulic acid. Thus 5-hydroxyferulic acid is formed from ferulic acid by the action of the specific enzyme ferulate 5-hydroxylase
16.
Sinapinic acid
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Sinapinic acid, or sinapic acid, is a small naturally occurring hydroxycinnamic acid. It is a member of the phenylpropanoid family and it is a commonly used matrix in MALDI mass spectrometry. It is a matrix for a wide variety of peptides. It serves well as a matrix for MALDI due to its ability to laser radiation. Sinapic acid can form dimers with itself and ferulic acid in cell walls. Sinapine is an alkaloidal amine found in mustard seeds. It is considered a choline ester of sinapic acid, sinapinic acid can be found in wine and vinegar. Sinapate 1-glucosyltransferase is an enzyme that uses UDP-glucose and sinapate to produce UDP, sinapoylglucose—malate O-sinapoyltransferase is an enzyme that uses 1-O-sinapoyl-beta-D-glucose and -malate to produce D-glucose and sinapoyl--malate. Canolol is a compound found in crude canola oil. It is produced by decarboxylation of sinapic acid during canola seed roasting
17.
Chlorogenic acid
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Chlorogenic acid is a natural chemical compound which is the ester of caffeic acid and -quinic acid. It is an important biosynthetic intermediate, chlorogenic acid is an important intermediate in lignin biosynthesis. This compound, known as an antioxidant, may also slow the release of glucose into the bloodstream after a meal, the term chlorogenic acids can also refer to a related family of esters of hydroxycinnamic acids with quinic acid. Despite the chloro of the name, chlorogenic acids contain no chlorine, instead, the name comes from the Greek χλωρός and -γένος, because of the green color produced when chlorogenic acids are oxidized. Structurally, chlorogenic acid is the ester formed between caffeic acid and the 3-hydroxyl position of L-quinic acid, isomers of chlorogenic acid include the caffeoyl ester at other hydroxyl sites on the quinic acid ring, 4-O-caffeoylquinic acid and 5-O-caffeoylquinic acid. The epimer at position 1 has not yet been reported and it should be noted that there is considerable ambiguity about the atom-numbering of chlorogenic acid. The order of numbering of atoms on the quinic acid ring was reversed in 1976 following IUPAC guidelines, with the consequence that 3-CQA became 5-CQA and this article uses the original numbering, which was exclusive prior to 1976. Thereafter researchers and manufacturers have been divided, with numbering systems in use. Even the 1976 IUPAC recommendations are not entirely satisfactory when applied to some of the less common chlorogenic acids, structures having more than one caffeic acid group are called isochlorogenic acids, and can be found in coffee. There are several isomers, such as 3, 4-dicaffeoylquinic acid and 3, 5-dicaffeoylquinic acid, chlorogenic acid is freely soluble in ethanol and acetone. Chlorogenic acid can be found in the bamboo Phyllostachys edulis. as well as in other plants. Chlorogenic acid can be found in the shoots of common heather, chlorogenic acid and the related compounds cryptochlorogenic acid, and neochlorogenic acid have been found in the leaves of Hibiscus sabdariffa, a popular tea product worldwide. Isomers of chlorogenic acid are found in potatoes, chlorogenic acid is the most abundant phenolic acid in the flesh of eggplants. It is one of the phenolic compounds identified in peach. It is also found in prunes and it also is one of the phenols found in green coffee bean extract and in green tea. Chlorogenic acid is marketed under the tradename Svetol, a green coffee extract, as a food additive used in coffee products, chewing gum, and mints. Dried sunflower leaves collected immediately after opening are processed into 98. 38% chlorogenic acid extract, review articles in 2011 and 2014 report modest blood pressure lowering effects from chlorogenic acid administration. No studies have appeared to assess possible interactions with drugs or advisability in patients being treated for low blood pressure
18.
Cynarine
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Cynarine is a hydroxycinnamic acid and a biologically active chemical constituent of artichoke. Chemically, it is a formed from quinic acid and two units of caffeic acid. It inhibits taste receptors, making water seem sweet and it is an ingredient of the drug Sulfad. List of drugs, Cp-Cz Chlorogenic acid
19.
Grape reaction product
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The grape reaction product is a phenolic compound explaining the disappearance of caftaric acid from grape must during processing. It is also found in aged red wines and its enzymatic production by polyphenol oxidase is important in limiting the browning of musts, especially in white wine production. The product can be recreated in model solutions and it is possible to determine its concentration in wine by mass spectrometry. S-Glutathionyl caftaric acid is itself oxidizable and it is not a substrate for grape polyphenol oxidase, but laccase from Botrytis cinerea can use it to form GRP2. Other related molecules are trans-caffeoyltartrate derivatives like GRP o-quinone and 2, 5-di-S-glutathionyl cafteoyl tartrate or adducts with anthocyanidins
20.
Ethyl caffeate
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Ethyl caffeate is an ester of an hydroxycinnamic acid, a naturally occurring organic compound. It can be found in Bidens pilosa, in Polygonum amplexicaule var. sinense and it is also found in wines such as Verdicchio, a white wine from Marche, Italy. Ethyl caffeate suppresses NF-kappaB activation and its downstream inflammatory mediators, iNOS, COX-2, ethyl caffeate administered intraperitoneally in rats previously is able to prevent the dimethylnitrosamine-induced loss in body and liver weight, as well as to reduce the degree of liver injury. It can be considered as a natural compound for future application in chronic liver disease. Ethyl caffeate reacts with methylamine to produce green pigments
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Caffeic acid phenethyl ester
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Caffeic acid phenethyl ester is a natural phenolic chemical compound. It is the ester of caffeic acid and phenethyl alcohol, CAPE is found in a variety of plants. It is also a component of propolis from honeybee hives, a variety of in vitro pharmacology and effects in animal models have been reported for CAPE, but their clinical significance is unknown. A study using CAPE showed an effect on reducing carcinogenic incidence. It is known to have antimitogenic, anticarcinogenic, anti-inflammatory, another study also showed that CAPE suppresses acute immune and inflammatory responses and holds promise for therapeutic uses to reduce inflammation. This anti-cancer effect was seen when mice skin was treated with bee propolis and exposed to TPA. CAPE significantly reduced the number of papillomas
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Rosmarinic acid
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Rosmarinic acid is a chemical compound found in a variety of plants. Rosmarinic acid was first isolated and characterized in 1958 by the Italian chemists M. L. Scarpatti and it is found most notably in many Lamiaceae, especially in the subfamily Nepetoideae. It is also found in other Lamiales such as Heliotropium foertherianum and it is also found in plants in the family Marantaceae such as species in the genera Maranta and Thalia. Rosmarinic acid and the derivative rosmarinic acid 3′-O-β-D-glucoside can be found in Anthoceros agrestis, the biosyntheses of rosmarinic acid uses 4-coumaroyl-CoA from the general phenylpropanoid pathway as hydroxycinnamoyl donor. The hydroxycinnamoyl acceptor substrate comes from the pathway, shikimic acid, quinic acid and 3. Thus, chemically, rosmarinic acid is an ester of caffeic acid with 3, 4-dihydroxyphenyllactic acid, rosmarinate synthase is an enzyme that uses caffeoyl-CoA and 3, 4-dihydroxyphenyllactic acid to produce CoA and rosmarinate. Hydroxyphenylpyruvate reductase is also an enzyme involved in this biosynthesis, the enzymes involved in the biosynthesis pathway probably evolved from those used in the formation of chlorogenic and caffeoylshikimic acids. In plants, rosmarinic acid is supposed to act as a preformed constitutively accumulated defense compound, rosmarinic acid is a potential anxiolytic as it acts as a GABA transaminase inhibitor, more specifically on 4-aminobutyrate transaminase. Rosmarinic acid also inhibits the expression of indoleamine 2, 3-dioxygenase via its cyclooxygenase-inhibiting properties, rosmarinic acid may remove the ciguatoxins from their sites of action. The use of acid is effective in a mouse model of Japanese encephalitis
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Echinacoside
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It is a caffeic acid glycoside from the phenylpropanoid class. This water-soluble glycoside is a secondary metabolite of Echinacea angustifolia and Echinacea pallida. It is also isolated from Cistanche spp and it was first isolated by Stoll et al. in 1950 from the roots of Echinacea angustifolia. It shows weak antibiotic activity in vitro against Staphylococcus aureus and Streptococci
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Verbascoside
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Verbascoside is a caffeoyl phenylethanoid glycoside. It is an ester formed with the phenylethanoid hydroxytyrosol, the phenylpropanoid caffeic acid, verbascoside can be found in species in all the families of the Lamiales order. Only two examples are known from outside the order, in the clade Asterids, verbascoside derivatives can be found in the Verbascum undulatum and notably apiosides in Verbascum sp. It can also be produced in plant cell cultures of Leucosceptrum sp and it can also be produced in hairy roots cultures of Paulownia tomentosa. Verbascoside has an activity, notably against Staphylococcus aureus. It can also have anti-inflammatory properties and it is a protein kinase C inhibitor
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Diferulic acids
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Diferulic acids are organic compounds that have the general chemical formula C20H18O8, they are formed by dimerisation of ferulic acid. Curcumin and curcuminoids, though having a structure resembling diferulic acids, are not formed that way, just as ferulic acid is not the proper IUPAC name, the diferulic acids also tend to have trivial names that are more commonly used than the correct IUPAC name. Diferulic acids are found in plant cell walls, particularly those of grasses, there are currently nine known structures for diferulic acids. They are usually named after the positions on each molecule that form the bond between them, included in the group are 8, 5-DiFA and 8, 8-DiFA, which are not true diferulic acids, but probably have a similar biological function. The 8, 5-DiFA lost CO2 during its formation, the 8, ferulic acid can also form trimers and tetramers, known as triferulic and tetraferulic acids respectively. They have been found in the walls of most plants. The 8-O-4-DiFA tends to predominate in grasses, but 5, 5-DiFA predomintes in barley bran, rye bread contains ferulic acid dehydrodimers. In chufa and sugar beet the predominant diferulic acids are 8-O-4-DiFA and 8, 8-5 Non cyclic diferulic acid has been identified to be covalently linked to carbohydrate moieties of the arabinogalactan-protein fraction of gum arabic. Diferulic acids are thought to have a function in plant cell walls. They have been extracted attached to a few molecules at both ends, but so far no definitive proof of them linking separate polysaccharide chains has been found. In suspension-cultured wheat cells, only the 8, 5-diferulic acid is formed intraprotoplasmically with the other dimers being formed in the cell wall, most diferulic acids are not commercially available and must be synthesised in lab. Synthetic routes have been published, but it is simpler to extract them from plant material. They can be extracted from plant cell walls by concentrated solutions of alkali, the resulting solution is evaporated to give a mixture of ferulic acid moieties that can be separated by column chromatography. Identification is often by high performance liquid chromatography with a UV detector or by LC-MS, alternatively they can be derivatised to make them volatile and therefore suitable for GC-MS. Curcumin can be hydrolyzed to two molecules of ferulic acid. Peroxidases can produce dimers of ferulic acid, in the presence of hydrogen peroxide through radical polymerization, diferulic acids are more effective inhibitors of lipid peroxidation and better scavengers of free radicals than ferulic acid on a molar basis. The first diferulic acid discovered was the 5, 5-diferulic acid, and for a while this was thought to be the only one
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8,5'-Diferulic acid
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8, 5-Diferulic acid is a non cyclic type of diferulic acid. It is the predominant diferulic acid in sugar beet pulp and it is also found in barley, in maize bran and rye. 8-5-Diferulic acid has also identified to be covalently linked to carbohydrate moieties of the arabinogalactan-protein fraction of gum arabic. Decarboxylated 8, 5-diferulic acid 5-8-Dehydrodiferulic acid at phenol-explorer. eu
