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.
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
3.
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
4.
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
5.
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
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.
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
8.
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
9.
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
10.
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
11.
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
12.
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
