1.
Acetal
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An acetal is a functional group with the following connectivity R2C2, where both R groups are organic fragments. The central carbon atom has four bonds to it, and is saturated and has tetrahedral geometry. The two RO groups may be equivalent to other or not. The two R groups can be equivalent to other or not, and one or both can even be hydrogen atoms rather than organic fragments. Acetals are formed from and convertible to carbonyl compounds, the term ketal is sometimes used to identify structures associated with ketones rather than aldehydes and, historically, the term acetal was used specifically for the aldehyde cases. Formation of an acetal occurs when the group of a hemiacetal becomes protonated and is lost as water. The carbocation that is produced is then attacked by a molecule of alcohol. Loss of the proton from the attached alcohol gives the acetal, acetals are stable compared to hemiacetals but their formation is a reversible equilibrium as with esters. As a reaction to create an acetal proceeds, water must be removed from the mixture, for example, with a Dean-Stark apparatus. The formation of acetals reduces the number of molecules present and therefore is not favourable with regards to entropy. A way to improve this is to use an orthoester as a source of alcohol, aldehydes and ketones undergo a process called acetal exchange with orthoesters to give acetals. Water produced along with the product is used up in hydrolysing the orthoester. Acetals are used as protecting groups for carbonyl groups in organic synthesis because they are stable with respect to hydrolysis by bases and they can either protect the carbonyl in a molecule or a diol. That is, either the carbonyl, or the alcohols, or both could be part of the molecule whose reactivity is to be controlled, various specific carbonyl compounds have special names for their acetal forms. For example, a formed from formaldehyde is sometimes called a formal or the methylenedioxy group. The acetal formed from acetone is sometimes called an acetonide, acetalisation is the organic reaction that involves the formation of an acetal. One way of formation is the nucleophilic addition of an alcohol to a ketone or an aldehyde. Acetalisation is often used in organic synthesis to create a group because it is a reversible reaction
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.
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
4.
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
5.
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
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.
Standard enthalpy of formation
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Its symbol is ΔHo f or ΔfHo. The superscript Plimsoll on this symbol indicates that the process has occurred under standard conditions at the specified temperature. One exception is phosphorus, for which the most stable form at 1 atm is black phosphorus and this is true for all enthalpies of formation. In physics the energy per particle is expressed in electronvolts. All elements in their states have a standard enthalpy of formation of zero. The formation reaction is a constant pressure and constant temperature process, since the pressure of the standard formation reaction is fixed at 1 atm, the standard formation enthalpy or reaction heat is a function of temperature. For tabulation purposes, standard formation enthalpies are all given at a temperature,298 K. The standard enthalpy of formation is equivalent to the sum of separate processes included in the Born–Haber cycle of synthesis reactions. This is because enthalpy is a state function, in the example above the standard enthalpy change of formation for sodium chloride is equal to the sum of the standard enthalpy change of formation for each of the steps involved in the process. This is especially useful for very long reactions with many intermediate steps, chemists may use standard enthalpies of formation for a reaction that is hypothetical. That it is shows that the reaction, if it were to proceed, would be exothermic. It is possible to heat of formations for simple unstrained organic compounds with the Heat of formation group additivity method. Standard enthalpies of formation are used in thermochemistry to find the enthalpy change of any reaction. This implies that the reaction is exothermic, the converse is also true, the standard enthalpy of reaction will be positive for an endothermic reaction. When a reaction is reversed, the magnitude of ΔH stays the same, when the balanced equation for a reaction is multiplied by an integer, the corresponding value of ΔH must be multiplied by that integer as well. Allotropes of an element other than the state generally have non-zero standard enthalpies of formation. Standard enthalpy of sublimation, or heat of sublimation, is defined as the required to sublime one mole of the substance under standard conditions. Standard enthalpy of solution is the change associated with the dissolution of a substance in a solvent at constant pressure under standard conditions
9.
Organic chemistry
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Study of structure includes many physical and chemical methods to determine the chemical composition and the chemical constitution of organic compounds and materials. In the modern era, the range extends further into the table, with main group elements, including, Group 1 and 2 organometallic compounds. They either form the basis of, or are important constituents of, many products including pharmaceuticals, petrochemicals and products made from them, plastics, fuels and explosives. Before the nineteenth century, chemists generally believed that compounds obtained from living organisms were endowed with a force that distinguished them from inorganic compounds. According to the concept of vitalism, organic matter was endowed with a vital force, during the first half of the nineteenth century, some of the first systematic studies of organic compounds were reported. Around 1816 Michel Chevreul started a study of soaps made from various fats and he separated the different acids that, in combination with the alkali, produced the soap. Since these were all compounds, he demonstrated that it was possible to make a chemical change in various fats, producing new compounds. In 1828 Friedrich Wöhler produced the chemical urea, a constituent of urine, from inorganic starting materials. The event is now accepted as indeed disproving the doctrine of vitalism. In 1856 William Henry Perkin, while trying to manufacture quinine accidentally produced the organic dye now known as Perkins mauve and his discovery, made widely known through its financial success, greatly increased interest in organic chemistry. A crucial breakthrough for organic chemistry was the concept of chemical structure, ehrlich popularized the concepts of magic bullet drugs and of systematically improving drug therapies. His laboratory made decisive contributions to developing antiserum for diphtheria and standardizing therapeutic serums, early examples of organic reactions and applications were often found because of a combination of luck and preparation for unexpected observations. The latter half of the 19th century however witnessed systematic studies of organic compounds, the development of synthetic indigo is illustrative. The production of indigo from plant sources dropped from 19,000 tons in 1897 to 1,000 tons by 1914 thanks to the methods developed by Adolf von Baeyer. In 2002,17,000 tons of indigo were produced from petrochemicals. In the early part of the 20th Century, polymers and enzymes were shown to be large organic molecules, the multiple-step synthesis of complex organic compounds is called total synthesis. Total synthesis of natural compounds increased in complexity to glucose. For example, cholesterol-related compounds have opened ways to synthesize complex human hormones, since the start of the 20th century, complexity of total syntheses has been increased to include molecules of high complexity such as lysergic acid and vitamin B12
10.
Moiety (chemistry)
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In organic chemistry moiety is a term used for part of a molecule. Larger moieties are often functional groups, a functional group is a moiety that participates in similar chemical reactions in most molecules that contain it. In turn the parts of the group are termed moieties, for example, methyl p-hydroxybenzoate contains a phenol functional group within the acyl moiety, which in turn is part of the paraben moiety. Moieties that are branches extending from the backbone of a hydrocarbon molecule, which can often be broken off and substituted with others, are called substituents or side chains
11.
Acyl group
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An acyl group is a moiety derived by the removal of one or more hydroxyl groups from an oxoacid, including inorganic acids. It contains a double bonded oxygen atom and an alkyl group, in organic chemistry, the acyl group is usually derived from a carboxylic acid. Therefore, it has the formula RCO–, where R represents a group that is linked to the carbon atom of the group by a single bond. Although the term is almost always applied to compounds, acyl groups can in principle be derived from other types of acids such as sulfonic acids. In the most common arrangement, acyl groups are attached to a molecular fragment, in which case the carbon. Well-known acyl compounds are the acyl chlorides, such as acetyl chloride and these compounds, which are treated as sources of acylium cations, are good reagents for attaching acyl groups to various substrates. Amides and esters are classes of compounds, as are ketones and aldehydes. Acylium ions are cations of the formula RCO+, such species are common reactive intermediates, for example, in the Friedel–Crafts acylations also in many other organic reactions such as the Hayashi rearrangement. Acylium cations are characteristic fragments observed in EI-mass spectra of ketones, acyl radicals are readily generated from aldehydes by H-atom abstraction. However, they undergo rapid decarbonylation to afford the alkyl radical, acyl anions are almost always unstable, usually too unstable to be exploited synthetically. Hence synthetic chemists have developed various acyl anion equivalents as surrogates, in biochemistry there are many instances of acyl groups, in all major categories of biochemical molecules. Acyl-CoAs are acyl derivatives formed via fatty acid metabolism, acetyl-CoA, the most common derivative, serves as an acyl donor in many biosynthetic transformations. Names of acyl groups of amino acids are formed by the replacement of the ending -ine by the ending -yl, for example, the acyl group of glycine is glycyl, and of lysine is lysyl. Names of acyl groups of ribonucleoside monophosphates such as AMP, GMP, CMP, and UMP are adenylyl, guanylyl, cytidylyl, in phospholipids, the acyl group of phosphatidic acid is called phosphatidyl-. Acyl ligands are intermediates in many reactions, which are important in some catalytic reactions. Metal acyls arise usually via insertion of carbon monoxide into metal–alkyl bonds, metal acyls also arise from reactions involving acyl chlorides with low-valence metal complexes or by the reaction of organolithium compounds with metal carbonyls. Metal acyls are often described by two structures, one of which emphasizes the basicity of the oxygen center. O-alkylation of metal acyls gives Fischer carbene complexes, the names of acyl groups are derived typically from the corresponding acid by substituting the acid ending -ic with the ending -yl as shown in the table below
12.
Skeletal formula
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A skeletal formula shows the skeletal structure or skeleton of a molecule, which is composed of the skeletal atoms that make up the molecule. It is represented in two dimensions, as on a page of paper and it employs certain conventions to represent carbon and hydrogen atoms, which are the most common in organic chemistry. The technique was developed by the organic chemist Friedrich August Kekulé von Stradonitz, Skeletal formulae have become ubiquitous in organic chemistry, partly because they are relatively quick and simple to draw. As in a Lewis structure, a doubled or tripled line segment indicates double or triple bonding, the skeletal structure of an organic compound is the series of atoms bonded together that form the essential structure of the compound. The skeleton can consist of chains, branches and/or rings of bonded atoms, Skeletal atoms other than carbon or hydrogen are called heteroatoms. The skeleton has hydrogen and/or various substituents bonded to its atoms, hydrogen is the most common non-carbon atom that is bonded to carbon and, for simplicity, is not explicitly drawn. For example, in the image below, the formula of hexane is shown. The carbon atom labeled C1 appears to have one bond. The carbon atom labelled C3 has two bonds to other carbons and is bonded to two hydrogen atoms as well. NOTE, It doesnt matter which end of the chain you start numbering from, the condensed formula or the IUPAC name will confirm the orientation. Some molecules will become familiar regardless of the orientation, any hydrogen atoms bonded to non-carbon atoms are drawn explicitly. In ethanol, C2H5OH, for instance, the hydrogen bonded to oxygen is denoted by the symbol H. Lines representing heteroatom-hydrogen bonds are usually omitted for clarity and compactness and these bonds are sometimes drawn out in full in order to accentuate their presence when they participate in reaction mechanisms. Shown below for comparison are a model of the actual three-dimensional structure of the ethanol molecule in the gas phase, the Lewis structure. All atoms that are not carbon or hydrogen are signified by their symbol, for instance Cl for chlorine, O for oxygen, Na for sodium. These atoms are known as heteroatoms in the context of organic chemistry. There are also symbols that appear to be chemical element symbols and these are known as pseudoelement symbols or organic elements. The most widely used symbol is Ph, which represents the phenyl group, boc for the t-butoxycarbonyl group Cbz or Z for the carboxybenzyl group Fmoc for the fluorenylmethoxycarbonyl group Two atoms can be bonded by sharing more than one pair of electrons
13.
Actinium
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Actinium is a radioactive chemical element with symbol Ac and atomic number 89, which was discovered in 1899. It was the first non-primordial radioactive element to be isolated, polonium, radium and radon were observed before actinium, but they were not isolated until 1902. Actinium gave the name to the series, a group of 15 similar elements between actinium and lawrencium in the periodic table. It is also considered the first of the 7th-period transition metals. A soft, silvery-white radioactive metal, actinium reacts rapidly with oxygen, as with most lanthanides and many actinides, actinium assumes oxidation state +3 in nearly all its chemical compounds. One tonne of uranium in ore contains about 0.2 milligrams of actinium-227. The close similarity of physical and chemical properties of actinium and lanthanum makes separation of actinium from the ore impractical, instead, the element is prepared, in milligram amounts, by the neutron irradiation of 226Ra in a nuclear reactor. Owing to its scarcity, high price and radioactivity, actinium has no significant industrial use and its current applications include a neutron source and an agent for radiation therapy targeting cancer cells in the body. André-Louis Debierne, a French chemist, announced the discovery of a new element in 1899 and he separated it from pitchblende residues left by Marie and Pierre Curie after they had extracted radium. In 1899, Debierne described the substance as similar to titanium, friedrich Oskar Giesel independently discovered actinium in 1902 as a substance being similar to lanthanum and called it emanium in 1904. Articles published in the 1970s and later suggest that Debiernes results published in 1904 conflict with those reported in 1899 and 1900 and this has led some authors to advocate that Giesel alone should be credited with the discovery. A less confrontational vision of scientific discovery is proposed by Adloff, Debierne, who is now considered by the vast majority of historians as the discoverer, lost interest in the element and left the topic. Giesel, on the hand, can rightfully be credited with the first preparation of radiochemically pure actinium. The name actinium originates from the Ancient Greek aktis, aktinos and its symbol Ac is also used in abbreviations of other compounds that have nothing to do with actinium, such as acetyl, acetate and sometimes acetaldehyde. Actinium is a soft, silvery-white, radioactive, metallic element and its estimated shear modulus is similar to that of lead. Owing to its radioactivity, actinium glows in the dark with a pale blue light. Actinium has similar properties to lanthanum and other lanthanides. Solvent extraction and ion chromatography are commonly used for the separation, the first element of the actinides, actinium gave the group its name, much as lanthanum had done for the lanthanides
14.
Methyl group
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A methyl group is an alkyl derived from methane, containing one carbon atom bonded to three hydrogen atoms — CH3. In formulas, the group is often abbreviated Me, such hydrocarbon groups occur in many organic compounds. It is a stable group in most molecules. While the methyl group is part of a larger molecule. The anion has eight electrons, the radical seven and the cation six. All three forms are highly reactive and rarely observed, the methylium cation exists in the gas phase, but is otherwise not encountered. Some compounds are considered to be sources of the CH3+ cation, the methanide anion exists only in rarefied gas phase or under exotic conditions. It can be produced by electrical discharge in ketene at low pressure, such reagents are generally prepared from the methyl halides, M + CH3X → MCH3 where M is an alkali metal. The methyl radical has the formula CH3 and it exists in dilute gases, but in more concentrated form it readily dimerizes to ethane. It can be produced by decomposition of only certain compounds. The reactivity of a methyl group depends on the adjacent substituents, methyl groups can be quite unreactive. For example, in compounds, the methyl group resists attack by even the strongest acids. The oxidation of a group occurs widely in nature and industry. The oxidation products derived from methyl are CH2OH, CHO, for example, permanganate often converts a methyl group to a carboxyl group, e. g. the conversion of toluene to benzoic acid. Ultimately oxidation of methyl groups gives protons and carbon dioxide, as seen in combustion, demethylation is a common process, and reagents that undergo this reaction are called methylating agents. Common methylating agents are dimethyl sulfate, methyl iodide, and methyl triflate, methanogenesis, the source of natural gas, arises via a demethylation reaction. Certain methyl groups can be deprotonated, for example, the acidity of the methyl groups in acetone is about 1020 more acidic than methane. The resulting carbanions are key intermediates in many reactions in organic synthesis and biosynthesis, fatty acids are produced in this way
15.
Carbonyl group
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In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom, C=O. It is common to several classes of compounds, as part of many larger functional groups. A compound containing a group is often referred to as a carbonyl compound. The term carbonyl can also refer to carbon monoxide as a ligand in an inorganic or organometallic complex, the remainder of this article concerns itself with the organic chemistry definition of carbonyl, where carbon and oxygen share a double bond. A carbonyl group characterizes the types of compounds, Note that the most specific labels are usually employed. For example, ROR structures are known as acid anhydride rather than the more generic ester, other organic carbonyls are urea and the carbamates, the derivatives of acyl chlorides chloroformates and phosgene, carbonate esters, thioesters, lactones, lactams, hydroxamates, and isocyanates. Examples of inorganic compounds are carbon dioxide and carbonyl sulfide. A special group of compounds are 1, 3-dicarbonyl compounds that have acidic protons in the central methylene unit. Examples are Meldrums acid, diethyl malonate and acetylacetone, because oxygen is more electronegative than carbon, carbonyl compounds often have resonance structures which affect their reactivity. This relative electronegativity draws electron density away from carbon, increasing the bonds polarity, carbon can then be attacked by nucleophiles or a negatively charged part of another molecule. During the reaction, the double bond is broken. This reaction is known as addition-elimination or condensation, the electronegative oxygen also can react with an electrophile, for example a proton in an acidic solution or with Lewis acids to form an oxocarbenium ion. The polarity of oxygen also makes the alpha hydrogens of carbonyl compounds much more acidic than typical sp3 C-H bonds, for example, the pKa values of acetaldehyde and acetone are 16.7 and 19 respectively, while the pKa value of methane is extrapolated to be approximately 50. This is because a carbonyl is in resonance with an enol. The deprotonation of the enol with a base produces an enolate. Amides are the most stable of the carbonyl couplings due to their high resonance stabilization between the nitrogen-carbon and carbon-oxygen bonds, carbonyl groups can be reduced by reaction with hydride reagents such as NaBH4 and LiAlH4, with bakers yeast, or by catalytic hydrogenation. Ketones give secondary alcohols while aldehydes, esters and carboxylic acids give primary alcohols, carbonyls can be alkylated in nucleophilic addition reactions using organometallic compounds such as organolithium reagents, Grignard reagents, or acetylides. Carbonyls also may be alkylated by enolates as in aldol reactions, carbonyls are also the prototypical groups with vinylogous reactivity
16.
Electron
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The electron is a subatomic particle, symbol e− or β−, with a negative elementary electric charge. Electrons belong to the first generation of the lepton particle family, the electron has a mass that is approximately 1/1836 that of the proton. Quantum mechanical properties of the include a intrinsic angular momentum of a half-integer value, expressed in units of the reduced Planck constant. As it is a fermion, no two electrons can occupy the same state, in accordance with the Pauli exclusion principle. Like all elementary particles, electrons exhibit properties of particles and waves, they can collide with other particles and can be diffracted like light. Since an electron has charge, it has an electric field. Electromagnetic fields produced from other sources will affect the motion of an electron according to the Lorentz force law, electrons radiate or absorb energy in the form of photons when they are accelerated. Laboratory instruments are capable of trapping individual electrons as well as electron plasma by the use of electromagnetic fields, special telescopes can detect electron plasma in outer space. Electrons are involved in applications such as electronics, welding, cathode ray tubes, electron microscopes, radiation therapy, lasers, gaseous ionization detectors. Interactions involving electrons with other particles are of interest in fields such as chemistry. The Coulomb force interaction between the positive protons within atomic nuclei and the negative electrons without, allows the composition of the two known as atoms, ionization or differences in the proportions of negative electrons versus positive nuclei changes the binding energy of an atomic system. The exchange or sharing of the electrons between two or more atoms is the cause of chemical bonding. In 1838, British natural philosopher Richard Laming first hypothesized the concept of a quantity of electric charge to explain the chemical properties of atoms. Irish physicist George Johnstone Stoney named this charge electron in 1891, electrons can also participate in nuclear reactions, such as nucleosynthesis in stars, where they are known as beta particles. Electrons can be created through beta decay of isotopes and in high-energy collisions. The antiparticle of the electron is called the positron, it is identical to the electron except that it carries electrical, when an electron collides with a positron, both particles can be totally annihilated, producing gamma ray photons. The ancient Greeks noticed that amber attracted small objects when rubbed with fur, along with lightning, this phenomenon is one of humanitys earliest recorded experiences with electricity. In his 1600 treatise De Magnete, the English scientist William Gilbert coined the New Latin term electricus, both electric and electricity are derived from the Latin ēlectrum, which came from the Greek word for amber, ἤλεκτρον
17.
Chemical bond
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A chemical bond is a lasting attraction between atoms that enables the formation of chemical compounds. The bond may result from the force of attraction between atoms with opposite charges, or through the sharing of electrons as in the covalent bonds. Since opposite charges attract via an electromagnetic force, the negatively charged electrons that are orbiting the nucleus. An electron positioned between two nuclei will be attracted to both of them, and the nuclei will be attracted toward electrons in this position and this attraction constitutes the chemical bond. This phenomenon limits the distance between nuclei and atoms in a bond, in general, strong chemical bonding is associated with the sharing or transfer of electrons between the participating atoms. All bonds can be explained by quantum theory, but, in practice, simplification rules allow chemists to predict the strength, directionality, the octet rule and VSEPR theory are two examples. Electrostatics are used to describe bond polarities and the effects they have on chemical substances, a chemical bond is an attraction between atoms. This attraction may be seen as the result of different behaviors of the outermost or valence electrons of atoms and these behaviors merge into each other seamlessly in various circumstances, so that there is no clear line to be drawn between them. However it remains useful and customary to differentiate different types of bond, which result in different properties of condensed matter. In the simplest view of a covalent bond, one or more electrons are drawn into the space between the two atomic nuclei, energy is released by bond formation. This is not as a reduction in energy, because the attraction of the two electrons to the two protons is offset by the electron-electron and proton-proton repulsions. In a polar covalent bond, one or more electrons are shared between two nuclei. Such weak intermolecular bonds give organic molecular substances, such as waxes and oils, their soft bulk character, also, the melting points of such covalent polymers and networks increase greatly. In a simplified view of a bond, the bonding electron is not shared at all. In this type of bond, the atomic orbital of one atom has a vacancy which allows the addition of one or more electrons. These newly added electrons potentially occupy a lower energy-state than they experience in a different atom, thus, one nucleus offers a more tightly bound position to an electron than does another nucleus, with the result that one atom may transfer an electron to the other. This transfer causes one atom to assume a net charge. The bond then results from electrostatic attraction between atoms and the atoms become positive or negatively charged ions, ionic bonds may be seen as extreme examples of polarization in covalent bonds
18.
IUPAC
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The International Union of Pure and Applied Chemistry /ˈaɪjuːpæk/ or /ˈjuːpæk/ is an international federation of National Adhering Organizations that represents chemists in individual countries. It is a member of the International Council for Science, IUPAC is registered in Zürich, Switzerland, and the administrative office, known as the IUPAC Secretariat, is in Research Triangle Park, North Carolina, United States. This administrative office is headed by IUPACs executive director, currently Lynn Soby, IUPAC was established in 1919 as the successor of the International Congress of Applied Chemistry for the advancement of chemistry. Its members, the National Adhering Organizations, can be national chemistry societies, national academies of sciences, there are fifty-four National Adhering Organizations and three Associate National Adhering Organizations. IUPACs Inter-divisional Committee on Nomenclature and Symbols is the world authority in developing standards for the naming of the chemical elements. Since its creation, IUPAC has been run by different committees with different responsibilities. These committees run different projects which include standardizing nomenclature, finding ways to bring chemistry to the world, IUPAC is best known for its works standardizing nomenclature in chemistry and other fields of science, but IUPAC has publications in many fields including chemistry, biology and physics. IUPAC is also known for standardizing the atomic weights of the elements through one of its oldest standing committees, the need for an international standard for chemistry was first addressed in 1860 by a committee headed by German scientist Friedrich August Kekulé von Stradonitz. This committee was the first international conference to create an international naming system for organic compounds, the ideas that were formulated in that conference evolved into the official IUPAC nomenclature of organic chemistry. IUPAC stands as a legacy of this meeting, making it one of the most important historical international collaborations of chemistry societies, since this time, IUPAC has been the official organization held with the responsibility of updating and maintaining official organic nomenclature. IUPAC as such was established in 1919, one notable country excluded from this early IUPAC is Germany. Germanys exclusion was a result of prejudice towards Germans by the Allied powers after World War I, Germany was finally admitted into IUPAC during 1929. However, Nazi Germany was removed from IUPAC during World War II, during World War II, IUPAC was affiliated with the Allied powers, but had little involvement during the war effort itself. After the war, East and West Germany were eventually readmitted to IUPAC, since World War II, IUPAC has been focused on standardizing nomenclature and methods in science without interruption. In 2016, IUPAC denounced the use of chlorine as a chemical weapon, the letter stated, Our organizations deplore the use of chlorine in this manner. According to the CWC, the use, stockpiling, distribution, IUPAC is governed by several committees that all have different responsibilities. Each committee is made up of members of different National Adhering Organizations from different countries, the steering committee hierarchy for IUPAC is as follows, All committees have an allotted budget to which they must adhere. Any committee may start a project, if a projects spending becomes too much for a committee to continue funding, it must take the issue to the Project Committee
19.
Organic compound
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An organic compound is virtually any chemical compound that contains carbon, although a consensus definition remains elusive and likely arbitrary. Organic compounds are rare terrestrially, but of importance because all known life is based on organic compounds. The most basic petrochemicals are considered the building blocks of organic chemistry, for historical reasons discussed below, a few types of carbon-containing compounds, such as carbides, carbonates, simple oxides of carbon, and cyanides are considered inorganic. The distinction between organic and inorganic compounds, while useful in organizing the vast subject of chemistry. Organic chemistry is the science concerned with all aspects of organic compounds, Organic synthesis is the methodology of their preparation. The word organic is historical, dating to the 1st century, for many centuries, Western alchemists believed in vitalism. This is the theory that certain compounds could be synthesized only from their classical elements—earth, water, air, vitalism taught that these organic compounds were fundamentally different from the inorganic compounds that could be obtained from the elements by chemical manipulation. Vitalism survived for a while even after the rise of modern atomic theory and it first came under question in 1824, when Friedrich Wöhler synthesized oxalic acid, a compound known to occur only in living organisms, from cyanogen. A more decisive experiment was Wöhlers 1828 synthesis of urea from the inorganic salts potassium cyanate, urea had long been considered an organic compound, as it was known to occur only in the urine of living organisms. Wöhlers experiments were followed by others, in which increasingly complex organic substances were produced from inorganic ones without the involvement of any living organism. Even though vitalism has been discredited, scientific nomenclature retains the distinction between organic and inorganic compounds, still, even the broadest definition requires excluding alloys that contain carbon, including steel. The C-H definition excludes compounds that are considered organic, neither urea nor oxalic acid is organic by this definition, yet they were two key compounds in the vitalism debate. The IUPAC Blue Book on organic nomenclature specifically mentions urea and oxalic acid, other compounds lacking C-H bonds but traditionally considered organic include benzenehexol, mesoxalic acid, and carbon tetrachloride. Mellitic acid, which contains no C-H bonds, is considered an organic substance in Martian soil. The C-H bond-only rule also leads to somewhat arbitrary divisions in sets of carbon-fluorine compounds, for example, CF4 would be considered by this rule to be inorganic, whereas CF3H would be organic. Organic compounds may be classified in a variety of ways, one major distinction is between natural and synthetic compounds. Another distinction, based on the size of organic compounds, distinguishes between small molecules and polymers, natural compounds refer to those that are produced by plants or animals. Many of these are extracted from natural sources because they would be more expensive to produce artificially
20.
Neurotransmitter
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Neurotransmitters, also known as chemical messengers, are endogenous chemicals that enable neurotransmission. They transmit signals across a synapse, such as a neuromuscular junction, from one neuron to another target neuron, muscle cell. Neurotransmitters are released from synaptic vesicles in synapses into the synaptic cleft, neurotransmitters play a major role in shaping everyday life and functions. Their exact numbers are unknown, but more than 100 chemical messengers have been uniquely identified, neurotransmitters are stored in a synapse in synaptic vesicles, clustered beneath the membrane in the axon terminal located at the presynaptic side of the synapse. Neurotransmitters are released into and diffused across the cleft, where they bind to specific receptors in the membrane on the postsynaptic side of the synapse. Most neurotransmitters are about the size of an amino acid, however. Nevertheless, short-term exposure of the receptor to a neurotransmitter is typically sufficient for causing a postsynaptic response by way of synaptic transmission, in response to a threshold action potential or graded electrical potential, a neurotransmitter is released at the presynaptic terminal. Low level baseline release also occurs without electrical stimulation, the released neurotransmitter may then move across the synapse to be detected by and bind with receptors in the postsynaptic neuron. Binding of neurotransmitters may influence the postsynaptic neuron in either an inhibitory or excitatory way and this neuron may be connected to many more neurons, and if the total of excitatory influences are greater than those of inhibitory influences, the neuron will also fire. Ultimately it will create a new action potential at its axon hillock to release neurotransmitters, until the early 20th century, scientists assumed that the majority of synaptic communication in the brain was electrical. However, through the careful histological examinations by Ramón y Cajal, upon completion of this experiment, Loewi asserted that sympathetic regulation of cardiac function can be mediated through changes in chemical concentrations. Furthermore, Otto Loewi is credited with discovering acetylcholine —the first known neurotransmitter, some neurons do, however, communicate via electrical synapses through the use of gap junctions, which allow specific ions to pass directly from one cell to another. There are four criteria for identifying neurotransmitters, The chemical must be synthesized in the neuron or otherwise be present in it. When the neuron is active, the chemical must be released, the same response must be obtained when the chemical is experimentally placed on the target. A mechanism must exist for removing the chemical from its site of activation after its work is done, have little or no effect on membrane voltage, but have a common carrying function such as changing the structure of the synapse. Communicate by sending messages that affect the release or reuptake of transmitters. Various techniques and experiments such as staining, stimulating, and collecting can be used to identify throughout the central nervous system. There are many different ways to classify neurotransmitters, dividing them into amino acids, peptides, and monoamines is sufficient for some classification purposes
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Acetylcholine
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Its name is derived from its chemical structure, it is an ester of acetic acid and choline. Parts in the body that use or are affected by acetylcholine are referred to as cholinergic, substances that interfere with acetylcholine activity are called anticholinergics. Acetylcholine is the used at the neuromuscular junction—in other words. This property means that drugs that affect cholinergic systems can have dangerous effects ranging from paralysis to convulsions. In the brain, acetylcholine functions as a neurotransmitter and as a neuromodulator, the brain contains a number of cholinergic areas, each with distinct functions. They play an important role in arousal, attention, memory, scopolamine, which acts mainly on muscarinic receptors in the brain, can cause delirium and amnesia. The addictive qualities of nicotine derive from its effects on nicotinic receptors in the brain. Acetylcholine has functions both in the nervous system and in the central nervous system. In the peripheral nervous system, acetylcholine activates muscles, and is a major neurotransmitter in the nervous system. In the CNS, cholinergic projections from the basal forebrain to the cerebral cortex, like many other biologically active substances, acetylcholine exerts its effects by binding to and activating receptors located on the surface of cells. There are two classes of acetylcholine receptor, nicotinic and muscarinic. Nicotinic acetylcholine receptors are ligand-gated ion channels permeable to sodium, potassium, in other words, they are ion channels embedded in cell membranes, capable of switching from a closed to open state when acetylcholine binds to them, in the open state they allow ions to pass through. Nicotinic receptors come in two types, known as muscle-type and neuronal-type. The muscle-type can be blocked by curare, the neuronal-type by hexamethonium. The main location of muscle-type receptors is on muscle cells, as described in detail below. Neuronal-type receptors are located in autonomic ganglia, and in the nervous system. Muscarinic acetylcholine receptors have a complex mechanism, and affect target cells over a longer time frame. In mammals, five subtypes of muscarinic receptors have been identified, labeled M1 through M5, all of them function as G protein-coupled receptors, meaning that they exert their effects via a second messenger system
22.
Acetylcysteine
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It can be taken intravenously, by mouth, or inhaled as a mist. Common side effects include nausea and vomiting when taken by mouth, the skin may occasionally become red and itchy with either form. A non immune type of anaphylaxis may also occur and it appears to be safe in pregnancy. It works by increasing glutathione levels and binding with the breakdown products of paracetamol. Acetylcysteine was initially patented in 1960 and licensed for use in 1968 and it is on the World Health Organizations List of Essential Medicines, the most effective and safe medicines needed in a health system. It is available as a medication and is not very expensive. Intravenous and oral formulations of acetylcysteine are available for the treatment of paracetamol overdose, when paracetamol is taken in large quantities, a minor metabolite called N-acetyl-p-benzoquinone imine accumulates within the body. It is normally conjugated by glutathione, but when taken in excess and this metabolite is then free to react with key hepatic enzymes, thereby damaging liver cells. This may lead to liver damage and even death by acute liver failure. In the treatment of acetaminophen overdose, acetylcysteine acts to maintain or replenish depleted glutathione reserves in the liver and these actions serve to protect liver cells from NAPQI toxicity. It is most effective in preventing or lessening hepatic injury when administered within 8–10 hours after overdose, research suggests that the rate of liver toxicity is approximately 3% when acetylcysteine is administered within 10 hours of overdose. Prior pharmacokinetic studies of acetylcysteine did not consider acetylation as a reason for the low bioavailability of acetylcysteine, oral acetylcysteine is identical in bioavailability to cysteine precursors. Repeated doses of intravenous acetylcysteine will cause these reactions to progressively worsen in these people. Several studies have found this anaphylaxis-like reaction to more often in people given IV acetylcysteine despite serum levels of paracetamol not high enough to be considered toxic. Inhaled acetylcysteine has been used for therapy in addition to other therapies in respiratory conditions with excessive and/or thick mucus production. It is also used post-operatively, as an aid. It may be considered ineffective in cystic fibrosis, a 2013 Cochrane review in cystic fibrosis found no evidence of benefit. Oral acetylcysteine is used for the prevention of radiocontrast-induced nephropathy, some studies show that prior administration of acetylcysteine decreases radiocontrast nephropathy, whereas others do not
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Acetylation
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Acetylation describes a reaction that introduces an acetyl functional group into a chemical compound. Deacetylation is the removal of an acetyl group, Acetylation refers to the process of introducing an acetyl group into a compound, namely the substitution of an acetyl group for an active hydrogen atom. A reaction involving the replacement of the atom of a hydroxyl group with an acetyl group yields a specific ester. Acetic anhydride is used as an acetylating agent reacting with free hydroxyl groups. For example, it is used in the synthesis of aspirin and heroin, Acetylation is an important modification of proteins in cell biology, and proteomics studies have identified thousands of acetylated mammalian proteins. Acetylation occurs as a co-translational and post-translational modification of proteins, for example, histones, p53, among these proteins, chromatin proteins and metabolic enzymes are highly represented, indicating that acetylation has a considerable impact on gene expression and metabolism. In bacteria, 90% of proteins involved in metabolism of Salmonella enteric are acetylated. N-terminal acetylation is one of the most common co-translational covalent modifications of proteins in eukaryotes, N-terminal acetylation plays an important role in the synthesis, stability and localization of proteins. About 85% of all proteins and 68% in yeast are acetylated at their Nα-terminus. Several proteins from prokaryotes and archaea are also modified by N-terminal acetylation, N-terminal Acetylation is catalyzed by a set of enzyme complexes, the N-terminal acetyltransferases. NATs transfer a group from acetyl-coenzyme A to the α-amino group of the first amino acid residue of the protein. Different NATs are responsible for the acetylation of nascent protein N-termini, to date, six different NATs have been found in humans - NatA, NatB, NatC, NatD, NatE and NatF. Each of these different enzyme complexes is specific for different amino acids or amino acid sequences which is shown in the following table, the Composition and Substrate specificity of NATs. NatA is composed of two subunits, the catalytic subunit Naa10 and the auxiliary subunit Naa15, NatA subunits are more complex in higher eukaryotes than in lower eukaryotes. In addition to the genes NAA10 and NAA15, the mammal-specific genes NAA11 and NAA16, make functional gene products, four possible hNatA catalytic-auxiliary dimers are formed by these four proteins. However, Naa10/Naa15 is the most abundant NatA, NatA acetylates Ser, Ala-, Gly-, Thr-, Val- and Cys N-termini after the initiator methionine is removed by methionine amino-peptidases. These amino acids are frequently expressed in the N-terminal of proteins in eukaryotes. Several different interaction partners are involved in the N-terminal acetylation by NatA, Huntingtin interacting protein K interacts with hNatA on the ribosome to affect the N-terminal acetylation of a subset of NatA substrates
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Citric acid cycle
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Its central importance to many biochemical pathways suggests that it was one of the earliest established components of cellular metabolism and may have originated abiogenically. The name of this pathway is derived from citric acid that is consumed. In addition, the cycle consumes acetate and water, reduces NAD+ to NADH, the NADH generated by the TCA cycle is fed into the oxidative phosphorylation pathway. The net result of two closely linked pathways is the oxidation of nutrients to produce usable chemical energy in the form of ATP. In eukaryotic cells, the citric acid cycle occurs in the matrix of the mitochondrion, components of the TCA cycle were derived from anaerobic bacteria, and the TCA cycle itself may have evolved more than once. Theoretically there are alternatives to the TCA cycle, however. If several TCA alternatives had evolved independently, they all appear to have converged to the TCA cycle, the citric acid cycle is a key metabolic pathway that connects carbohydrate, fat, and protein metabolism. The reactions of the cycle are carried out by 8 enzymes that completely oxidize acetate, in the form of acetyl-CoA, through catabolism of sugars, fats, and proteins, the two-carbon organic product acetyl-CoA is produced which enters the citric acid cycle. The NADH and FADH2 generated by the citric acid cycle are in used by the oxidative phosphorylation pathway to generate energy-rich adenosine triphosphate. Acetyl-CoA may also be obtained from the oxidation of fatty acids, the citrate then goes through a series of chemical transformations, losing two carboxyl groups as CO2. The carbons lost as CO2 originate from what was oxaloacetate, not directly from acetyl-CoA, the carbons donated by acetyl-CoA become part of the oxaloacetate carbon backbone after the first turn of the citric acid cycle. Loss of the acetyl-CoA-donated carbons as CO2 requires several turns of the citric acid cycle. However, because of the role of the citric acid cycle in anabolism, they not be lost. Most of the energy available by the oxidative steps of the cycle is transferred as energy-rich electrons to NAD+. For each acetyl group that enters the citric cycle, three molecules of NADH are produced. Electrons are also transferred to the electron acceptor Q, forming QH2, at the end of each cycle, the four-carbon oxaloacetate has been regenerated, and the cycle continues. Two carbon atoms are oxidized to CO2, the energy from these reactions is transferred to other processes through GTP. The NADH generated in the TCA cycle may later be oxidized to drive ATP synthesis in a type of process called oxidative phosphorylation, FADH2 is covalently attached to succinate dehydrogenase, an enzyme which functions both in the CAC and the mitochondrial electron transport chain in oxidative phosphorylation
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Pyruvate dehydrogenase
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Pyruvate dehydrogenase is the first component enzyme of pyruvate dehydrogenase complex. The pyruvate dehydrogenase complex contributes to transforming pyruvate into acetyl-CoA by a process called pyruvate decarboxylation, pyruvate dehydrogenase performs the first two reactions within the pyruvate dehydrogenase complex, a decarboxylation of substrate 1 and a reductive acetylation of substrate 2. Lipoic acid is bound to dihydrolipoamide acetyltransferase, which is the second catalytic component enzyme of PDC. The reaction catalyzed by pyruvate dehydrogenase is considered to be the step for the pyruvate dehydrogenase complex. Phosphorylation of E1 by pyruvate dehydrogenase kinase inactivates E1 and subsequently the entire complex, PDK is inhibited by dichloroacetic acid and pyruvate, resulting in a higher quantity of active, unphosphorylated PDH. Phosphorylaton is reversed by pyruvate dehydrogenase phosphatase, which is stimulated by insulin, PEP, and AMP, but competitively inhibited by ATP, NADH, the ylide resonance form of thiamine pyrophosphate begins by attacking the electrophilic ketone of pyruvate. This 1, 3-dipole undergoes a reductive acetylation with lipoamide-E2 and this unique combination of contacts and conformations of TPP leads to formation of the reactive C2-carbanion, eventually. After the cofactor TPP decarboxylates pyruvate, the acetyl portion becomes a hydroxyethyl derivative covalently attached to TPP, mammalian E1s, including human E1, are tetrameric, composed of two α- and two β- subunits. Some bacterial E1s, including E1 from Escherichia coli, are composed of two subunits, each being as large as the sum of molecular masses of α-. E1 has two sites, each providing thiamine pyrophosphate and magnesium ion as cofactors. The α- subunit binds magnesium ion and pyrophosphate fragment while the β-subunit binds pyrimidine fragment of TPP, the active site for pyruvate dehydrogenase holds TPP through metal ligation to a magnesium ion and through hydrogen bonding to amino acids. The amino acids are shown as wires, and the TPP is in ball, the active site also aids in the transfer of the acyl on the TPP to a lipoamide waiting on E2. Pyruvate dehydrogenase is an autoantigen recognized in primary biliary cirrhosis and these antibodies appear to recognize oxidized protein that has resulted from inflammatory immune responses. Other mitochondrial autoantigens include oxoglutarate dehydrogenase and branched-chain alpha-keto acid dehydrogenase complex, pyruvate dehydrogenase deficiency is a congenital degenerative metabolic disease resulting from a mutation of the pyruvate dehydrogenase complex located on the X chromosome. While defects have been identified in all 3 enzymes of the complex, malfunction of the citric acid cycle due to PDH deficiency deprives the body of energy and leads to an abnormal buildup of lactate. PDH deficiency is a cause of lactic acidosis in newborns and often presents with severe lethargy, poor feeding, tachypnea. In E. coli this enzyme is encoded by the pox B gene and this enzyme increases the efficiency of growth of E. coli under aerobic conditions
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Pyruvic acid
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Pyruvic acid is the simplest of the alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the base, CH3COCOO−, is a key intermediate in several metabolic pathways. Pyruvic acid can be made from glucose through glycolysis, converted back to carbohydrates via gluconeogenesis and it can also be used to construct the amino acid alanine and can be converted into ethanol or lactic acid via fermentation. Pyruvic acid supplies energy to cells through the citric acid cycle when oxygen is present, pyruvic acid is a colorless liquid with a smell similar to that of acetic acid and is miscible with water. It is the output of the metabolism of known as glycolysis. One molecule of glucose breaks down into two molecules of pyruvate, which are used to provide further energy, in one of two ways. Pyruvate is converted into acetyl-coenzyme A, which is the input for a series of reactions known as the Krebs cycle. Pyruvate is also converted to oxaloacetate by an reaction, which replenishes Krebs cycle intermediates, also. These reactions are named after Hans Adolf Krebs, the biochemist awarded the 1953 Nobel Prize for physiology, jointly with Fritz Lipmann, for research into metabolic processes. The cycle is known as the citric acid cycle or tricarboxylic acid cycle. If insufficient oxygen is available, the acid is broken down anaerobically, creating lactate in animals and ethanol in plants, Pyruvate is a key intersection in the network of metabolic pathways. Pyruvate can be converted into carbohydrates via gluconeogenesis, to fatty acids or energy through acetyl-CoA, to the amino acid alanine, therefore, it unites several key metabolic processes. In glycolysis, phosphoenolpyruvate is converted to pyruvate by pyruvate kinase and this reaction is strongly exergonic and irreversible, in gluconeogenesis, it takes two enzymes, pyruvate carboxylase and PEP carboxykinase, to catalyze the reverse transformation of pyruvate to PEP. Compound C00074 at KEGG Pathway Database, enzyme 2.7.1.40 at KEGG Pathway Database. Compound C00022 at KEGG Pathway Database, click on genes, proteins and metabolites below to link to respective articles. Pyruvate decarboxylation by the pyruvate dehydrogenase complex produces acetyl-CoA, carboxylation by pyruvate carboxylase produces oxaloacetate. Transamination by alanine transaminase produces alanine, reduction by lactate dehydrogenase produces lactate. Pyruvate is sold as a supplement, though evidence supporting this use is lacking
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Histone
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In biology, histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the protein components of chromatin, acting as spools around which DNA winds. Without histones, the unwound DNA in chromosomes would be very long, five major families of histones exist, H1/H5, H2A, H2B, H3, and H4. Histones H2A, H2B, H3 and H4 are known as the core histones, the core histones all exist as dimers, which are similar in that they all possess the histone fold domain, three alpha helices linked by two loops. It is this structure that allows for interaction between distinct dimers, particularly in a head-tail fashion. The resulting four distinct dimers then come together to form one octameric nucleosome core, around 146 base pairs of DNA wrap around this core particle 1.65 times in a left-handed super-helical turn to give a particle of around 100 Angstroms across. The linker histone H1 binds the nucleosome at the entry and exit sites of the DNA, thus locking the DNA into place, the most basic such formation is the 10 nm fiber or beads on a string conformation. This involves the wrapping of DNA around nucleosomes with approximately 50 base pairs of DNA separating each pair of nucleosomes, higher-order structures include the 30 nm fiber and 100 nm fiber, these being the structures found in normal cells. During mitosis and meiosis, the chromosomes are assembled through interactions between nucleosomes and other regulatory proteins. In animals, genes encoding canonical histones are typically clustered along the chromosome, lack introns, genes encoding histone variants are usually not clustered, have introns and their mRNAs are regulated with polyA tails. Complex multicellular organisms typically have a number of histone variants providing a variety of different functions. Recent data are accumulating about the roles of diverse histone variants highlighting the links between variants and the delicate regulation of organism development. Histone variants from different organisms, their classification and variant specific features can be found in HistoneDB2.0 - Variants database. The following is a list of human proteins, The nucleosome core is formed of two H2A-H2B dimers and a H3-H4 tetramer, forming two nearly symmetrical halves by tertiary structure. The H2A-H2B dimers and H3-H4 tetramer also show pseudodyad symmetry, the 4 core histones are relatively similar in structure and are highly conserved through evolution, all featuring a helix turn helix turn helix motif. They also share the feature of long tails on one end of the amino acid structure - this being the location of post-translational modification, despite the differences in their topology, these three folds share a homologous helix-strand-helix motif. Using an electron paramagnetic resonance spin-labeling technique, British researchers measured the distances between the spools around which eukaryotic cells wind their DNA and they determined the spacings range from 59 to 70 Å. Histones are subject to post translational modification by enzymes primarily on their N-terminal tails, such modifications include methylation, citrullination, acetylation, phosphorylation, SUMOylation, ubiquitination, and ADP-ribosylation
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Protein
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Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, a linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide, short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds, the sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the code specifies 20 standard amino acids, however. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors, proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes. Once formed, proteins only exist for a period of time and are then degraded and recycled by the cells machinery through the process of protein turnover. A proteins lifespan is measured in terms of its half-life and covers a wide range and they can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal and or misfolded proteins are degraded more rapidly due to being targeted for destruction or due to being unstable. Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms, many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized, digestion breaks the proteins down for use in the metabolism. Methods commonly used to study structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance. Most proteins consist of linear polymers built from series of up to 20 different L-α-amino acids, all proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group, a carboxyl group, and a variable side chain are bonded. Only proline differs from this structure as it contains an unusual ring to the N-end amine group. The amino acids in a chain are linked by peptide bonds. Once linked in the chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen. The peptide bond has two forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are roughly coplanar
29.
Transcription (biology)
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Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA by the enzyme RNA polymerase. Both DNA and RNA are nucleic acids, which use base pairs of nucleotides as a complementary language, during transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel RNA strand called a primary transcript. Transcription proceeds in the general steps, RNA polymerase, together with one or more general transcription factors. RNA polymerase creates a bubble, which separates the two strands of the DNA helix. This is done by breaking the bonds between complementary DNA nucleotides. RNA sugar-phosphate backbone forms with assistance from RNA polymerase to form an RNA strand, hydrogen bonds of the RNA–DNA helix break, freeing the newly synthesized RNA strand. If the cell has a nucleus, the RNA may be further processed and this may include polyadenylation, capping, and splicing. The RNA may remain in the nucleus or exit to the cytoplasm through the pore complex. The stretch of DNA transcribed into an RNA molecule is called a transcription unit, if the gene encodes a protein, the transcription produces messenger RNA, the mRNA, in turn, serves as a template for the proteins synthesis through translation. Alternatively, the gene may encode for either non-coding RNA, ribosomal RNA, transfer RNA. Overall, RNA helps synthesize, regulate, and process proteins, in virology, the term may also be used when referring to mRNA synthesis from an RNA molecule. For instance, the genome of a negative-sense single-stranded RNA virus may be template for a positive-sense single-stranded RNA and this is because the positive-sense strand contains the information needed to translate the viral proteins for viral replication afterwards. This process is catalyzed by a viral RNA replicase, the regulatory sequence before the coding sequence is called the five prime untranslated region, the sequence after the coding sequence is called the three prime untranslated region. As opposed to DNA replication, transcription results in an RNA complement that includes the nucleotide uracil in all instances where thymine would have occurred in a DNA complement, only one of the two DNA strands serve as a template for transcription. The antisense strand of DNA is read by RNA polymerase from the 3 end to the 5 end during transcription. The complementary RNA is created in the direction, in the 5 →3 direction. This directionality is because RNA polymerase can only add nucleotides to the 3 end of the growing mRNA chain and this use of only the 3 →5 DNA strand eliminates the need for the Okazaki fragments that are seen in DNA replication. This also removes the need for an RNA primer to initiate RNA synthesis, the non-template strand of DNA is called the coding strand, because its sequence is the same as the newly created RNA transcript
30.
Histone deacetylase
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Histone deacetylases are a class of enzymes that remove acetyl groups from an ε-N-acetyl lysine amino acid on a histone, allowing the histones to wrap the DNA more tightly. This is important because DNA is wrapped around histones, and DNA expression is regulated by acetylation and de-acetylation and its action is opposite to that of histone acetyltransferase. HDAC proteins are now also called lysine deacetylases, to describe their function rather than their target, together with the acetylpolyamine amidohydrolases and the acetoin utilization proteins, the histone deacetylases form an ancient protein superfamily known as the histone deacetylase superfamily. HDACs, are classified in four classes depending on sequence homology to the yeast original enzymes and domain organization, HDAC proteins are grouped into four classes based on function and DNA sequence similarity. Class IV contains just one isoform, which is not highly homologous with either Rpd3 or hda1 yeast enzymes, and therefore HDAC11 is assigned to its own class. The Class III enzymes are considered a type of enzyme and have a different mechanism of action. Within the Class I HDACs, HDAC1,2, and 3 are found primarily in the nucleus, Class II HDACs are able to shuttle in and out of the nucleus, depending on different signals. HDAC6 is a cytoplasmic, microtuble-associated enzyme, HDAC6 deacetylates tubulin, Hsp90, and cortactin, and forms complexes with other partner proteins, and is, therefore, involved in a variety of biological processes. Histone tails are normally positively charged due to amine groups present on their lysine and arginine amino acids and these positive charges help the histone tails to interact with and bind to the negatively charged phosphate groups on the DNA backbone. Acetylation, which occurs normally in a cell, neutralizes the positive charges on the histone by changing amines into amides and decreases the ability of the histones to bind to DNA and this decreased binding allows chromatin expansion, permitting genetic transcription to take place. Histone deacetylases remove those acetyl groups, increasing the positive charge of histone tails, the increased DNA binding condenses DNA structure, preventing transcription. Histone deacetylase is involved in a series of pathways within the living system, hyperacetylated chromatin is transcriptionally active, and hypoacetylated chromatin is silent. A study on mice found that a subset of mouse genes was deregulated in the absence of HDAC1. Their study also found a regulatory crosstalk between HDAC1 and HDAC2 and suggest a function for HDAC1 as a transcriptional coactivator. HDAC1 expression was found to be increased in the cortex of schizophrenia subjects. It is a mistake to regard HDACs solely in the context of regulating transcription by modifying histones and chromatin structure. The function, activity, and stability of proteins can be controlled by post-translational modifications, the acetylation of lysine residues is emerging as an analogous mechanism, in which non-histone proteins are acted on by acetylases and deacetylases. It is in context that HDACs are being found to interact with a variety of non-histone proteins—some of these are transcription factors and co-regulators
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DNA methylation
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DNA methylation is a process by which methyl groups are added to the DNA molecule. Methylation can change the activity of a DNA segment without changing the sequence, when located in a gene promoter, DNA methylation typically acts to repress gene transcription. Two of DNAs four bases, cytosine and adenine, can be methylated. 3% in Escherichia coli,0. 03% in Drosophila, adenine methylation has been observed in bacterial, plant and recently in mammalian DNA, but have received considerably less attention. In plants and other organisms, DNA methylation is found in three different sequence contexts, CG, CHG or CHH, in mammals however, DNA methylation is almost exclusively found in CpG dinucleotides, with the cytosines on both strand being usually methylated. Non-CpG methylation can however be observed in embryonic cells, and has also been indicated in neural development. Furthermore, non-CpG methylation has also observed in hematopoietic progenitor cells. The DNA methylation landscape of vertebrates is very particular compared to other organisms, in vertebrates, around 60-80% of CpG are methylated in somatic cells and DNA methylation appears as a default state that has to be specifically excluded from defined locations. High CpG methylation in mammalian genomes has an evolutionary cost because it increases the frequency of spontaneous mutations, loss of amino-groups occurs with a high frequency for cytosines, with different consequences depending on their methylation. Excluding repeated sequences, there are around 25,000 CpG islands in the human genome and they are major regulatory units and around 50% of CpG islands are located in gene promoter regions, while another 25% lie in gene bodies, often serving as alternative promoters. Reciprocally, around 60-70% of human genes have a CpG island in their promoter region, the majority of CpG islands are constitutively unmethylated and enriched for permissive chromatin modification such as H3K4 methylation. In somatic tissues, only 10% of CpG islands are methylated, DNA methylation was probably present at some extent in very early eukaryote ancestors. In virtually every organism analyzed, methylation in promoter regions correlates negatively with gene expression, cpG-dense promoters of actively transcribed genes are never methylated, but reciprocally transcriptionally silent genes do not necessarily carry a methylated promoter. DNA methylation may affect the transcription of genes in two ways and this link between DNA methylation and chromatin structure is very important. DNA methylation is a transcriptional repressor, at least in CpG dense contexts. Transcriptional repression of protein-coding genes appears essentially limited to specific classes of genes that need to be silent permanently. While DNA methylation does not have the flexibility required for the fine-tuning of gene regulation, transposon control is one the most ancient function of DNA methylation that is shared by animals, plants and multiple protists. It is even suggested that DNA methylation evolved precisely for this purpose, a function that appears even more conserved than transposon silencing is positively correlated with gene expression. In almost all species where DNA methylation is present, DNA methylation is especially enriched in the body of highly transcribed genes, the function of gene body methylation is not well understood
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Acetic anhydride
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Acetic anhydride, or ethanoic anhydride, is the chemical compound with the formula 2O. Commonly abbreviated Ac2O, it is the simplest isolable anhydride of an acid and is widely used as a reagent in organic synthesis. It is a liquid that smells strongly of acetic acid. Acetic anhydride, like most acid anhydrides, is a molecule with a nonplanar structure. The pi system linkage through the central oxygen offers very weak resonance stabilization compared to the repulsion between the two carbonyl oxygens. The energy barriers to rotation between each of the optimal aplanar conformations are quite low. Like most acid anhydrides, the carbon of acetic anhydride has electrophilic character. Acetic anhydride was first synthesized in 1852 by the French chemist Charles Frédéric Gerhardt by heating potassium acetate with benzoyl chloride, carbonylation of the methyl iodide in turn affords acetyl iodide, which reacts with acetate salts or acetic acid to give the product. Rhodium chloride in the presence of iodide is employed as catalysts. Because acetic anhydride is not stable in water, the conversion is conducted under anhydrous conditions, to a decreasing extent, acetic anhydride is also prepared by the reaction of ketene with acetic acid at 45–55 °C and low pressure. Due to its low cost, acetic anhydride is purchased, not prepared, acetic anhydride is a versatile reagent for acetylations, the introduction of acetyl groups to organic substrates. In these conversions, acetic anhydride is viewed as a source of CH3CO+, alcohols and amines are readily acetylated. For example, the reaction of acetic anhydride with ethanol yields ethyl acetate, in specialized applications, Lewis acidic scandium salts have also proven effective catalysts. Aromatic rings are acetylated by acetic anhydride, usually acid catalysts are used to accelerate the reaction. It is also used for the preparation of mixed anhydrides such as that with nitric acid, aldehydes react with acetic anhydride in the presence of an acidic catalyst to give geminal diacetates. 6% by weight. Aqueous solutions have limited stability because, like most acid anhydrides, in this case, acetic acid is formed, 2O + H2O →2 CH3CO2H As indicated by its organic chemistry, Ac2O is mainly used for acetylations leading to commercially significant materials. Similarly it is used in the production of aspirin, which is prepared by the acetylation of salicylic acid and it is also used as a wood preservative via autoclave impregnation to make a longer-lasting timber. S. DEA List II precursor, and restricted in other countries
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Acetyl chloride
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Acetyl chloride, CH3COCl is an acid chloride derived from acetic acid. It belongs to the class of compounds called acyl halides. It is a colorless, corrosive, volatile liquid, acetyl chloride was first prepared in 1852 by French chemist Charles Gerhardt by reacting potassium acetate with phosphoryl chloride. However, these methods usually gives acetyl chloride contaminated by phosphorus or sulfur impurities, a route avoiding these impurities of phosphorus and sulphur is that of phosgene and acetic acid, COCl2 + CH3COOH = CH3COCl + HCl + CO2. HCl impurities can be removed by distilling the product from dimethylaniline or by degassing the mixture by a stream of argon. When heated, a mixture of acid and acetic acid gives acetyl chloride. It can also be synthesized from the catalytic carbonylation of methyl chloride, acetyl chloride is not expected to exist in nature, because contact with water would hydrolyze it into acetic acid and hydrogen chloride. In fact, if handled in air it releases white smoke resulting from hydrolysis due to the moisture in the air. The smoke is actually small droplets of hydrochloric acid and acetic acid formed by hydrolysis, acetyl chloride is used for acetylation reactions, i. e. the introduction of an acetyl group. Acetyl is a group having the formula-C-CH3. For further information on the types of chemical compounds such as acetyl chloride can undergo. Two major classes of acetylations include esterification and the Friedel-Crafts reaction, acetyl chloride is a reagent for the preparation of esters and amides of acetic acid, used in the derivatization of alcohols and amines. One class of reactions are esterification. Such reactions will often proceed via ketene, a second major class of acetylation reactions are the Friedel-Crafts reactions
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Amine
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In organic chemistry, amines are compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are formally derivatives of ammonia, wherein one or more hydrogen atoms have been replaced by a substituent such as an alkyl or aryl group, important amines include amino acids, biogenic amines, trimethylamine, and aniline, see Category, Amines for a list of amines. Inorganic derivatives of ammonia are also called amines, such as chloramine, see Category, compounds with a nitrogen atom attached to a carbonyl group, thus having the structure R–CO–NR′R″, are called amides and have different chemical properties from amines. An aliphatic amine has no aromatic ring attached directly to the nitrogen atom, aromatic amines have the nitrogen atom connected to an aromatic ring as in the various anilines. The aromatic ring decreases the alkalinity of the amine, depending on its substituents, the presence of an amine group strongly increases the reactivity of the aromatic ring, due to an electron-donating effect. Amines are organized into four subcategories, Primary amines — Primary amines arise when one of three atoms in ammonia is replaced by an alkyl or aromatic. Important primary alkyl amines include, methylamine, most amino acids, Secondary amines — Secondary amines have two organic substituents bound to the nitrogen together with one hydrogen. Important representatives include dimethylamine, while an example of an aromatic amine would be diphenylamine, tertiary amines — In tertiary amines, nitrogen has three organic substituents. Examples include trimethylamine, which has a fishy smell. Cyclic amines — Cyclic amines are either secondary or tertiary amines, examples of cyclic amines include the 3-membered ring aziridine and the six-membered ring piperidine. N-methylpiperidine and N-phenylpiperidine are examples of tertiary amines. It is also possible to have four organic substituents on the nitrogen and these species are not amines but are quaternary ammonium cations and have a charged nitrogen center. Quaternary ammonium salts exist with many kinds of anions, Amines are named in several ways. Typically, the compound is given the prefix amino- or the suffix, the prefix N- shows substitution on the nitrogen atom. An organic compound with multiple amino groups is called a diamine, triamine, tetraamine, systematic names for some common amines, Hydrogen bonding significantly influences the properties of primary and secondary amines. Thus the melting point and boiling point of amines is higher than those of the corresponding phosphines, for example, methyl and ethyl amines are gases under standard conditions, whereas the corresponding methyl and ethyl alcohols are liquids. Amines possess a characteristic smell, liquid amines have a distinctive fishy smell. The nitrogen atom features a lone pair that can bind H+ to form an ammonium ion R3NH+
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