1.
Aconitase
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Aconitase is an enzyme that catalyses the stereo-specific isomerization of citrate to isocitrate via cis-aconitate in the tricarboxylic acid cycle, a non-redox-active process. Aconitase, displayed in the structures in the margin of this page, has two slightly different structures, depending on whether it is activated or inactivated. In the inactive form, its structure is divided into four domains, the Fe-S cluster and a SO42− anion also reside in the active site. When the enzyme is activated, it gains an additional iron atom, however, the structure of the rest of the enzyme is nearly unchanged, the conserved atoms between the two forms are in essentially the same positions, up to a difference of 0.1 angstroms. In contrast with the majority of proteins that function as electron carriers. Aconitase has an active 2+ cluster, which may convert to an inactive + form, three cysteine residues have been shown to be ligands of the centre. In the active state, the iron ion of the cluster is not coordinated by Cys. The iron-responsive element-binding protein and 3-isopropylmalate dehydratase, an enzyme catalysing the second step in the biosynthesis of leucine, are known aconitase homologues, iron regulatory elements constitute a family of 28-nucleotide, non-coding, stem-loop structures that regulate iron storage, heme synthesis and iron uptake. They also participate in ribosome binding and control the mRNA turnover, the specific regulator protein, the IRE-BP, binds to IREs in both 5 and 3 regions, but only to RNA in the apo form, without the Fe-S cluster. Mutant IRE-BPs, in any or all of the three Cys residues involved in Fe-S formation are replaced by serine, have no aconitase activity. Aconitase is inhibited by fluoroacetate, therefore fluoroacetate is poisonous, fluoroacetate, in the citric acid cycle, can innocently enter as fluorocitrate. However, aconitase cannot bind this substrate and thus the citric acid cycle is halted, the iron sulfur cluster is highly sensitive to oxidation by superoxide. The catalytic residues involved are His-101 and Ser-642, at this point, the intermediate is rotated 180°. This rotation is referred to as a flip, because of this flip, the intermediate is said to move from a citrate mode to a isocitrate mode. How exactly this flip occurs is debatable, one theory is that, in the rate-limiting step of the mechanism, the cis-aconitate is released from the enzyme, then reattached in the isocitrate mode to complete the reaction. This rate-liming step ensures that the right stereochemistry, specifically, is formed in the final product, another hypothesis is that cis-aconitate stays bound to the enzyme while it flips from the citrate to the isocitrate mode. In either case, flipping cis-aconitate allows the dehydration and hydration steps to occur on faces of the intermediate. Aconitase catalyzes trans elimination/addition of water, and the guarantees that the correct stereochemistry is formed in the product
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.
ChEMBL
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ChEMBL or ChEMBLdb is a manually curated chemical database of bioactive molecules with drug-like properties. It is maintained by the European Bioinformatics Institute, of the European Molecular Biology Laboratory, based at the Wellcome Trust Genome Campus, Hinxton, the database, originally known as StARlite, was developed by a biotechnology company called Inpharmatica Ltd. later acquired by Galapagos NV. The data was acquired for EMBL in 2008 with an award from The Wellcome Trust, resulting in the creation of the ChEMBL chemogenomics group at EMBL-EBI, the ChEMBL database contains compound bioactivity data against drug targets. Bioactivity is reported in Ki, Kd, IC50, and EC50, data can be filtered and analyzed to develop compound screening libraries for lead identification during drug discovery. ChEMBL version 2 was launched in January 2010, including 2.4 million bioassay measurements covering 622,824 compounds and this was obtained from curating over 34,000 publications across twelve medicinal chemistry journals. ChEMBLs coverage of available bioactivity data has grown to become the most comprehensive ever seen in a public database, in October 2010 ChEMBL version 8 was launched, with over 2.97 million bioassay measurements covering 636,269 compounds. ChEMBL_10 saw the addition of the PubChem confirmatory assays, in order to integrate data that is comparable to the type, ChEMBLdb can be accessed via a web interface or downloaded by File Transfer Protocol. It is formatted in a manner amenable to computerized data mining, ChEMBL is also integrated into other large-scale chemistry resources, including PubChem and the ChemSpider system of the Royal Society of Chemistry. In addition to the database, the ChEMBL group have developed tools and these include Kinase SARfari, an integrated chemogenomics workbench focussed on kinases. The system incorporates and links sequence, structure, compounds and screening data, the primary purpose of ChEMBL-NTD is to provide a freely accessible and permanent archive and distribution centre for deposited data. July 2012 saw the release of a new data service, sponsored by the Medicines for Malaria Venture. The data in this service includes compounds from the Malaria Box screening set, myChEMBL, the ChEMBL virtual machine, was released in October 2013 to allow users to access a complete and free, easy-to-install cheminformatics infrastructure. In December 2013, the operations of the SureChem patent informatics database were transferred to EMBL-EBI, in a portmanteau, SureChem was renamed SureChEMBL. 2014 saw the introduction of the new resource ADME SARfari - a tool for predicting and comparing cross-species ADME targets
4.
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
5.
European Chemicals Agency
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ECHA is the driving force among regulatory authorities in implementing the EUs chemicals legislation. ECHA helps companies to comply with the legislation, advances the safe use of chemicals, provides information on chemicals and it is located in Helsinki, Finland. The Agency, headed by Executive Director Geert Dancet, started working on 1 June 2007, the REACH Regulation requires companies to provide information on the hazards, risks and safe use of chemical substances that they manufacture or import. Companies register this information with ECHA and it is freely available on their website. So far, thousands of the most hazardous and the most commonly used substances have been registered, the information is technical but gives detail on the impact of each chemical on people and the environment. This also gives European consumers the right to ask whether the goods they buy contain dangerous substances. The Classification, Labelling and Packaging Regulation introduces a globally harmonised system for classifying and labelling chemicals into the EU. This worldwide system makes it easier for workers and consumers to know the effects of chemicals, companies need to notify ECHA of the classification and labelling of their chemicals. So far, ECHA has received over 5 million notifications for more than 100000 substances, the information is freely available on their website. Consumers can check chemicals in the products they use, Biocidal products include, for example, insect repellents and disinfectants used in hospitals. The Biocidal Products Regulation ensures that there is information about these products so that consumers can use them safely. ECHA is responsible for implementing the regulation, the law on Prior Informed Consent sets guidelines for the export and import of hazardous chemicals. Through this mechanism, countries due to hazardous chemicals are informed in advance and have the possibility of rejecting their import. Substances that may have effects on human health and the environment are identified as Substances of Very High Concern 1. These are mainly substances which cause cancer, mutation or are toxic to reproduction as well as substances which persist in the body or the environment, other substances considered as SVHCs include, for example, endocrine disrupting chemicals. Companies manufacturing or importing articles containing these substances in a concentration above 0 and they are required to inform users about the presence of the substance and therefore how to use it safely. Consumers have the right to ask the retailer whether these substances are present in the products they buy, once a substance has been officially identified in the EU as being of very high concern, it will be added to a list. This list is available on ECHA’s website and shows consumers and industry which chemicals are identified as SVHCs, Substances placed on the Candidate List can then move to another list
6.
IUPHAR/BPS
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The IUPHAR/BPS Guide to PHARMACOLOGY is an open-access website, acting as a portal to information on the biological targets of licensed drugs and other small molecules. The Guide to PHARMACOLOGY is developed as a joint venture between the International Union of Basic and Clinical Pharmacology and the British Pharmacological Society and this replaces and expands upon the original 2009 IUPHAR Database. The information featured includes pharmacological data, target and gene nomenclature, overviews and commentaries on each target family are included, with links to key references. The Guide to PHARMACOLOGY was initially made available online in December 2011 with additional material released in July 2012 and its network of over 700 specialist advisors contribute expertise and data. The current PI and Grant holder of the GtoPdb project is Prof. Jamie A. Davies, the development and release of the first version of the GtoPdb in 2012 was described in an editorial published in the British Journal of Pharmacology entitled Guide to Pharmacology. org- an update. The IUPHAR-DB is no longer being developed and all the contained within this site is now available through the Guide to PHARMACOLOGY. A complete list of all the approved drugs included on the website is available via the ligand list. The Guide to PHARMACOLOGY is being expanded to include information on targets and ligands. Search features on the website include quick and advanced search options, other features include Hot topic news items and a recent receptor-ligand pairing list. A hard copy summary of the database is published as The Concise Guide to Pharmacology 2015/2016 as a series of papers as a bi-annual supplement to the British Journal of Pharmacology. The Guide to PHARMACOLOGY includes links to other relevant resources via target, many of these resources maintain reciprocal links with the relevant Guide to PHARMACOLOGY pages. As of November 2015 the Wellcome Trust is supporting a new project to develop the Guide to Immumopharmacology, the latter continues to be supported by the British Pharmacological Society
7.
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
8.
International Chemical Identifier
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Initially developed by IUPAC and NIST from 2000 to 2005, the format and algorithms are non-proprietary. The continuing development of the standard has supported since 2010 by the not-for-profit InChI Trust. The current version is 1.04 and was released in September 2011, prior to 1.04, the software was freely available under the open source LGPL license, but it now uses a custom license called IUPAC-InChI Trust License. Not all layers have to be provided, for instance, the layer can be omitted if that type of information is not relevant to the particular application. InChIs can thus be seen as akin to a general and extremely formalized version of IUPAC names and they can express more information than the simpler SMILES notation and differ in that every structure has a unique InChI string, which is important in database applications. Information about the 3-dimensional coordinates of atoms is not represented in InChI, the InChI algorithm converts input structural information into a unique InChI identifier in a three-step process, normalization, canonicalization, and serialization. The InChIKey, sometimes referred to as a hashed InChI, is a fixed length condensed digital representation of the InChI that is not human-understandable. The InChIKey specification was released in September 2007 in order to facilitate web searches for chemical compounds and it should be noted that, unlike the InChI, the InChIKey is not unique, though collisions can be calculated to be very rare, they happen. In January 2009 the final 1.02 version of the InChI software was released and this provided a means to generate so called standard InChI, which does not allow for user selectable options in dealing with the stereochemistry and tautomeric layers of the InChI string. The standard InChIKey is then the hashed version of the standard InChI string, the standard InChI will simplify comparison of InChI strings and keys generated by different groups, and subsequently accessed via diverse sources such as databases and web resources. Every InChI starts with the string InChI= followed by the version number and this is followed by the letter S for standard InChIs. The remaining information is structured as a sequence of layers and sub-layers, the layers and sub-layers are separated by the delimiter / and start with a characteristic prefix letter. The six layers with important sublayers are, Main layer Chemical formula and this is the only sublayer that must occur in every InChI. The atoms in the formula are numbered in sequence, this sublayer describes which atoms are connected by bonds to which other ones. Describes how many hydrogen atoms are connected to each of the other atoms, the condensed,27 character standard InChIKey is a hashed version of the full standard InChI, designed to allow for easy web searches of chemical compounds. Most chemical structures on the Web up to 2007 have been represented as GIF files, the full InChI turned out to be too lengthy for easy searching, and therefore the InChIKey was developed. With all databases currently having below 50 million structures, such duplication appears unlikely at present, a recent study more extensively studies the collision rate finding that the experimental collision rate is in agreement with the theoretical expectations. Example, Morphine has the structure shown on the right, as the InChI cannot be reconstructed from the InChIKey, an InChIKey always needs to be linked to the original InChI to get back to the original structure
9.
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
10.
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
11.
Melting point
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The melting point of a solid is the temperature at which it changes state from solid to liquid at atmospheric pressure. At the melting point the solid and liquid phase exist in equilibrium, the melting point of a substance depends on pressure and is usually specified at standard pressure. When considered as the temperature of the change from liquid to solid. Because of the ability of some substances to supercool, the point is not considered as a characteristic property of a substance. For most substances, melting and freezing points are approximately equal, for example, the melting point and freezing point of mercury is 234.32 kelvins. However, certain substances possess differing solid-liquid transition temperatures, for example, agar melts at 85 °C and solidifies from 31 °C to 40 °C, such direction dependence is known as hysteresis. The melting point of ice at 1 atmosphere of pressure is close to 0 °C. In the presence of nucleating substances the freezing point of water is the same as the melting point, the chemical element with the highest melting point is tungsten, at 3687 K, this property makes tungsten excellent for use as filaments in light bulbs. Many laboratory techniques exist for the determination of melting points, a Kofler bench is a metal strip with a temperature gradient. Any substance can be placed on a section of the strip revealing its thermal behaviour at the temperature at that point, differential scanning calorimetry gives information on melting point together with its enthalpy of fusion. A basic melting point apparatus for the analysis of crystalline solids consists of an oil bath with a transparent window, the several grains of a solid are placed in a thin glass tube and partially immersed in the oil bath. The oil bath is heated and with the aid of the melting of the individual crystals at a certain temperature can be observed. In large/small devices, the sample is placed in a heating block, the measurement can also be made continuously with an operating process. For instance, oil refineries measure the point of diesel fuel online, meaning that the sample is taken from the process. This allows for more frequent measurements as the sample does not have to be manually collected, for refractory materials the extremely high melting point may be determined by heating the material in a black body furnace and measuring the black-body temperature with an optical pyrometer. For the highest melting materials, this may require extrapolation by several hundred degrees, the spectral radiance from an incandescent body is known to be a function of its temperature. An optical pyrometer matches the radiance of a body under study to the radiance of a source that has been previously calibrated as a function of temperature, in this way, the measurement of the absolute magnitude of the intensity of radiation is unnecessary. However, known temperatures must be used to determine the calibration of the pyrometer, for temperatures above the calibration range of the source, an extrapolation technique must be employed
12.
Aqueous solution
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An aqueous solution is a solution in which the solvent is water. It is usually shown in chemical equations by appending to the relevant chemical formula, for example, a solution of table salt, or sodium chloride, in water would be represented as Na+ + Cl−. The word aqueous means pertaining to, related to, similar to, as water is an excellent solvent and is also naturally abundant, it is a ubiquitous solvent in chemistry. Substances that are hydrophobic often do not dissolve well in water, an example of a hydrophilic substance is sodium chloride. Acids and bases are aqueous solutions, as part of their Arrhenius definitions, the ability of a substance to dissolve in water is determined by whether the substance can match or exceed the strong attractive forces that water molecules generate between themselves. If the substance lacks the ability to dissolve in water the molecules form a precipitate, reactions in aqueous solutions are usually metathesis reactions. Metathesis reactions are another term for double-displacement, that is, when a cation displaces to form a bond with the other anion. The cation bonded with the latter anion will dissociate and bond with the other anion, aqueous solutions that conduct electric current efficiently contain strong electrolytes, while ones that conduct poorly are considered to have weak electrolytes. Those strong electrolytes are substances that are ionized in water. Nonelectrolytes are substances that dissolve in water yet maintain their molecular integrity, examples include sugar, urea, glycerol, and methylsulfonylmethane. When writing the equations of reactions, it is essential to determine the precipitate. To determine the precipitate, one must consult a chart of solubility, soluble compounds are aqueous, while insoluble compounds are the precipitate. Remember that there may not always be a precipitate, when performing calculations regarding the reacting of one or more aqueous solutions, in general one must know the concentration, or molarity, of the aqueous solutions. Solution concentration is given in terms of the form of the prior to it dissolving. Metal ions in aqueous solution Solubility Dissociation Acid-base reaction theories Properties of water Zumdahl S.1997, 4th ed. Boston, Houghton Mifflin Company
13.
Alkaloid
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Alkaloids are a group of naturally occurring chemical compounds that mostly contain basic nitrogen atoms. This group also includes some related compounds with neutral and even weakly acidic properties, some synthetic compounds of similar structure are also termed alkaloids. In addition to carbon, hydrogen and nitrogen, alkaloids may also contain oxygen, sulfur and, more rarely, other such as chlorine, bromine. Alkaloids are produced by a variety of organisms including bacteria, fungi, plants. They can be purified from crude extracts of these organisms by acid-base extraction, many have found use in traditional or modern medicine, or as starting points for drug discovery. Other alkaloids possess psychotropic and stimulant activities, and have used in entheogenic rituals or as recreational drugs. Although alkaloids act on a diversity of systems in humans and other animals. The boundary between alkaloids and other nitrogen-containing natural compounds is not clear-cut, Compounds like amino acid peptides, proteins, nucleotides, nucleic acid, amines, and antibiotics are usually not called alkaloids. Natural compounds containing nitrogen in the position are usually classified as amines rather than as alkaloids. Some authors, however, consider alkaloids a special case of amines, the name alkaloids was introduced in 1819 by the German chemist Carl Friedrich Wilhelm Meißner, and is derived from late Latin root Latin, alkali and the suffix Greek, -οειδής – like. However, the term came into use only after the publication of a review article by Oscar Jacobsen in the chemical dictionary of Albert Ladenburg in the 1880s. There is no method of naming alkaloids. Many individual names are formed by adding the suffix ine to the species or genus name, for example, atropine is isolated from the plant Atropa belladonna, strychnine is obtained from the seed of Strychnine tree. If several alkaloids are extracted from one plant then their names often contain suffixes idine, anine, aline, inine etc. There are also at least 86 alkaloids whose names contain the root vin because they are extracted from plants such as Vinca rosea. Alkaloid-containing plants have been used by humans since ancient times for therapeutic, for example, medicinal plants have been known in the Mesopotamia at least around 2000 BC. The Odyssey of Homer referred to a given to Helen by the Egyptian queen. It is believed that the gift was an opium-containing drug, a Chinese book on houseplants written in 1st–3rd centuries BC mentioned a medical use of Ephedra and opium poppies
14.
Aconitum
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These herbaceous perennial plants are chiefly native to the mountainous parts of the Northern Hemisphere, growing in the moisture-retentive but well-draining soils of mountain meadows. Most species are poisonous and must be dealt with carefully. The dark green leaves of Aconitum species lack stipules and they are palmate or deeply palmately lobed with five to seven segments. Each segment again is trilobed with coarse sharp teeth, the leaves have a spiral arrangement. The lower leaves have long petioles, the tall, erect stem is crowned by racemes of large blue, purple, white, yellow, or pink zygomorphic flowers with numerous stamens. They are distinguishable by having one of the five sepals, called the galea, in the form of a cylindrical helmet. Two to 10 petals are present, the two upper petals are large and are placed under the hood of the calyx and are supported on long stalks. They have a spur at their apex, containing the nectar. The other petals are small and scale-like or nonforming, the three to five carpels are partially fused at the base. The fruit is an aggregate of follicles, a follicle being a dry, Aconitum species have been recorded as food plant of the caterpillars of several moths. The yellow tiger moth Arctia flavia, and the purple-shaded gem Euchalcia variabilis are at home on A. vulparia, the purple-lined sallow Pyrrhia exprimens, and Blepharita amica were found eating from A. septentrionale. The dot moth Melanchra persicariae occurs both on A. septentrionale and A. intermedium, the golden plusia Polychrysia moneta is hosted by A. vulparia, A. napellus, A. septentrionale, and A. intermedium. Other moths associated with Aconitum species include the wormwood pug Eupithecia absinthiata, satyr pug E. satyrata, Aterpia charpentierana and it is also the primary food source for the Old World bumblebee Bombus consobrinus. The roots of A. ferox supply the Nepalese poison called bikh, bish and it contains large quantities of the alkaloid pseudaconitine, which is a deadly poison. A. palmatum yields another of the bikh poisons, the root of A. luridum, of the Himalaya, is said to be as poisonous as that of A. ferox or A. napellus. Several species of Aconitum have been used as arrow poisons, the Minaro in Ladakh use A. napellus on their arrows to hunt ibex, while the Ainu in Japan used a species of Aconitum to hunt bear. The Chinese also used Aconitum poisons both for hunting and for warfare, Aconitum poisons were used by the Aleuts of Alaskas Aleutian Islands for hunting whales. Usually, one man in an armed with a poison-tipped lance would hunt the whale, paralyzing it with the poison
15.
China
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China, officially the Peoples Republic of China, is a unitary sovereign state in East Asia and the worlds most populous country, with a population of over 1.381 billion. The state is governed by the Communist Party of China and its capital is Beijing, the countrys major urban areas include Shanghai, Guangzhou, Beijing, Chongqing, Shenzhen, Tianjin and Hong Kong. China is a power and a major regional power within Asia. Chinas landscape is vast and diverse, ranging from forest steppes, the Himalaya, Karakoram, Pamir and Tian Shan mountain ranges separate China from much of South and Central Asia. The Yangtze and Yellow Rivers, the third and sixth longest in the world, respectively, Chinas coastline along the Pacific Ocean is 14,500 kilometers long and is bounded by the Bohai, Yellow, East China and South China seas. China emerged as one of the worlds earliest civilizations in the basin of the Yellow River in the North China Plain. For millennia, Chinas political system was based on hereditary monarchies known as dynasties, in 1912, the Republic of China replaced the last dynasty and ruled the Chinese mainland until 1949, when it was defeated by the communist Peoples Liberation Army in the Chinese Civil War. The Communist Party established the Peoples Republic of China in Beijing on 1 October 1949, both the ROC and PRC continue to claim to be the legitimate government of all China, though the latter has more recognition in the world and controls more territory. China had the largest economy in the world for much of the last two years, during which it has seen cycles of prosperity and decline. Since the introduction of reforms in 1978, China has become one of the worlds fastest-growing major economies. As of 2016, it is the worlds second-largest economy by nominal GDP, China is also the worlds largest exporter and second-largest importer of goods. China is a nuclear weapons state and has the worlds largest standing army. The PRC is a member of the United Nations, as it replaced the ROC as a permanent member of the U. N. Security Council in 1971. China is also a member of numerous formal and informal multilateral organizations, including the WTO, APEC, BRICS, the Shanghai Cooperation Organization, the BCIM, the English name China is first attested in Richard Edens 1555 translation of the 1516 journal of the Portuguese explorer Duarte Barbosa. The demonym, that is, the name for the people, Portuguese China is thought to derive from Persian Chīn, and perhaps ultimately from Sanskrit Cīna. Cīna was first used in early Hindu scripture, including the Mahābhārata, there are, however, other suggestions for the derivation of China. The official name of the state is the Peoples Republic of China. The shorter form is China Zhōngguó, from zhōng and guó and it was then applied to the area around Luoyi during the Eastern Zhou and then to Chinas Central Plain before being used as an occasional synonym for the state under the Qing
16.
Analgesic
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An analgesic or painkiller is any member of the group of drugs used to achieve analgesia, relief from pain. Analgesic drugs act in various ways on the peripheral and central nervous systems and they are distinct from anesthetics, which temporarily affect, and in some instances completely eliminate, sensation. Analgesics include paracetamol, the nonsteroidal anti-inflammatory drugs such as the salicylates, when choosing analgesics, the severity and response to other medication determines the choice of agent, the World Health Organization pain ladder specifies mild analgesics as its first step. Topical nonsteroidal anti-inflammatory drugs provided pain relief in common such as muscle sprains. Since the side effects are also lesser, topical preparations could be preferred over oral medications in these conditions, each different type of analgesic has its own associated side effects. Drugs for pain are typically classified by chemical structure and they may also be classified in other ways. Sometimes they are classified by use for classes of medical condition. Other times they are sorted by the needs of populations who would use them. They might be listed by availability in an area, perhaps to prevent recommending a drug which is illegal in one place even if it is easily available elsewhere. Paracetamol, also known as acetaminophen or APAP, is a used to treat pain. It is typically used for mild to moderate pain, in combination with opioid pain medication, paracetamol is used for more severe pain such as cancer pain and after surgery. It is typically used either by mouth or rectally but is also available intravenously, effects last between two and four hours. Paracetamol is classified as a mild analgesic, paracetamol is generally safe at recommended doses. Nonsteroidal anti-inflammatory drugs, are a class that groups together drugs that provide analgesic and antipyretic effects. The most prominent members of group of drugs, aspirin. These drugs have been derived from NSAIDs, the cyclooxygenase enzyme inhibited by NSAIDs was discovered to have at least 2 different versions, COX1 and COX2. Research suggested most of the effects of NSAIDs to be mediated by blocking the COX1 enzyme. Thus, the COX2 inhibitors were developed to inhibit only the COX2 enzyme and these drugs are equally effective analgesics when compared with NSAIDs, but cause less gastrointestinal hemorrhage in particular
17.
Antipyretic
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Antipyretics are substances that reduce fever. Antipyretics cause the hypothalamus to override a prostaglandin-induced increase in temperature, the body then works to lower the temperature, which results in a reduction in fever. Most antipyretic medications have other purposes, there is some debate over the appropriate use of such medications, as fever is part of the bodys immune response to infection. A study published by the Royal Society claims fever suppression causes at least 1% more influenza cases of death, bathing or sponging with lukewarm or cool water can effectively reduce body temperature in those with heat illness, but not usually in those with fever. The use of baths is not an appropriate cooling method. Traditional use of plants with antipyretic properties is a common worldwide feature of many ethnobotanical cultural systems. In ethnobotany, plants with naturally occurring antipyretic properties are commonly referred to as febrifuges, the U. S. Food and Drug Administration notes that improper dosing is one of the biggest problems in giving acetaminophen to children. The effectiveness of acetaminophen alone as an antipyretic in children is uncertain, therapies involving alternating doses of acetaminophen and ibuprofen have shown greater antipyretic effect than either drug alone. One meta-analysis indicated that ibuprofen is more effective than acetaminophen in children at similar doses when both are given alone, due to concerns about Reye syndrome, the U. K. NHS, the U. S. However, the use of aspirin, with the converse increased use of acetaminophen/paracetamol, has been linked to the increase in asthma. Physicians recommending acetaminophen/paracetamol should use caution and be attentive to any genetic or environmental predisposition to asthma or other autoimmune disorders. Antipyretic was the word spelled by Joanne Lagatta to win the 1991 Scripps National Spelling Bee, on the second disc for the Final Fantasy Tactics soundtrack, there is a track titled Antipyretic
18.
Delphinium
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Delphinium is a genus of about 300 species of perennial flowering plants in the family Ranunculaceae, native throughout the Northern Hemisphere and also on the high mountains of tropical Africa. All members of the Delphinium genus are toxic to humans and livestock, the common name larkspur is shared between perennial Delphinium species and annual species of the genus Consolida. Molecular data show that Consolida, as well as another segregate genus, the name delphinium derives from the Latin for dolphin, referring to the shape of the nectary. The leaves are deeply lobed with three to seven toothed, pointed lobes in a palmate shape. The main flowering stem is erect, and varies greatly in size between the species, from 10 centimetres in some species, up to 2 m tall in the larger meadowland species. In June and July, the plant is topped with a raceme of flowers, varying in color from purple and blue, to red, yellow. In most species each flower consists of five sepals which grow together to form a hollow pocket with a spur at the end. Within the sepals are four petals, small, inconspicuous. The eponymous long spur of the upper sepal encloses the nectar-containing spurs of the two upper petals, the seeds are small and often shiny black. The plants flower from spring to late summer, and are pollinated by butterflies. Despite the toxicity, Delphinium species are used as food plants by the larvae of some Lepidoptera species, including the dot moth, genetic analysis suggests that Delphinium sensu lato, as it was delineated before the 21st century, is polyphyletic. Nested within Delphinium s. l. are Aconitella, Consolida, to make Delphinium monophyletic, several interventions were made. The new genus Staphisagria was erected containing Delphinium staphisagria, D. requini, further genetic analysis has shown that the two large subgenera Aconitum and Aconitum are the sister group to Aconitum gymnandrum, Delphinium, Delphinium, Consolida and Aconitella. To make Aconitum monophyletic, A. gymnandrum has now been reassigned to a new monotypic genus, finally, Consolida and Aconitella are synonymized with Delphinium. D. arthriscifolium is sister to all species of Delphinium sensu stricto. It should be placed in its own subgenus, but no proposal naming this subgenus has been made yet, the subgenera Delphinium and Delphinium are sister to the group consisting of the species of Consolida and Aconitella, which together make up the subgenus Delphinium. Aconitella cannot be retained as a subgenus because A. barbata does not cluster with the species previously assigned to that genus. Pictum = Staphisagria picta D. requienii = Staphisagria requienii D. staphisagria = Staphisagria staphisagria Delphiniums can attract butterflies, various delphiniums are cultivated as ornamental plants, for traditional and native plant gardens
19.
Water
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Water is a transparent and nearly colorless chemical substance that is the main constituent of Earths streams, lakes, and oceans, and the fluids of most living organisms. Its chemical formula is H2O, meaning that its molecule contains one oxygen, Water strictly refers to the liquid state of that substance, that prevails at standard ambient temperature and pressure, but it often refers also to its solid state or its gaseous state. It also occurs in nature as snow, glaciers, ice packs and icebergs, clouds, fog, dew, aquifers, Water covers 71% of the Earths surface. It is vital for all forms of life. Only 2. 5% of this water is freshwater, and 98. 8% of that water is in ice and groundwater. Less than 0. 3% of all freshwater is in rivers, lakes, and the atmosphere, a greater quantity of water is found in the earths interior. Water on Earth moves continually through the cycle of evaporation and transpiration, condensation, precipitation. Evaporation and transpiration contribute to the precipitation over land, large amounts of water are also chemically combined or adsorbed in hydrated minerals. Safe drinking water is essential to humans and other even though it provides no calories or organic nutrients. There is a correlation between access to safe water and gross domestic product per capita. However, some observers have estimated that by 2025 more than half of the population will be facing water-based vulnerability. A report, issued in November 2009, suggests that by 2030, in developing regions of the world. Water plays an important role in the world economy, approximately 70% of the freshwater used by humans goes to agriculture. Fishing in salt and fresh water bodies is a source of food for many parts of the world. Much of long-distance trade of commodities and manufactured products is transported by boats through seas, rivers, lakes, large quantities of water, ice, and steam are used for cooling and heating, in industry and homes. Water is an excellent solvent for a variety of chemical substances, as such it is widely used in industrial processes. Water is also central to many sports and other forms of entertainment, such as swimming, pleasure boating, boat racing, surfing, sport fishing, Water is a liquid at the temperatures and pressures that are most adequate for life. Specifically, at atmospheric pressure of 1 bar, water is a liquid between the temperatures of 273.15 K and 373.15 K
20.
Alcohol
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In chemistry, an alcohol is any organic compound in which the hydroxyl functional group is bound to a saturated carbon atom. The term alcohol originally referred to the alcohol ethanol, the predominant alcohol in alcoholic beverages. The suffix -ol in non-systematic names also typically indicates that the substance includes a functional group and, so. But many substances, particularly sugars contain hydroxyl functional groups without using the suffix, an important class of alcohols, of which methanol and ethanol are the simplest members is the saturated straight chain alcohols, the general formula for which is CnH2n+1OH. The word alcohol is from the Arabic kohl, a used as an eyeliner. Al- is the Arabic definite article, equivalent to the in English, alcohol was originally used for the very fine powder produced by the sublimation of the natural mineral stibnite to form antimony trisulfide Sb 2S3, hence the essence or spirit of this substance. It was used as an antiseptic, eyeliner, and cosmetic, the meaning of alcohol was extended to distilled substances in general, and then narrowed to ethanol, when spirits as a synonym for hard liquor. Bartholomew Traheron, in his 1543 translation of John of Vigo, Vigo wrote, the barbarous auctours use alcohol, or alcofoll, for moost fine poudre. The 1657 Lexicon Chymicum, by William Johnson glosses the word as antimonium sive stibium, by extension, the word came to refer to any fluid obtained by distillation, including alcohol of wine, the distilled essence of wine. Libavius in Alchymia refers to vini alcohol vel vinum alcalisatum, Johnson glosses alcohol vini as quando omnis superfluitas vini a vino separatur, ita ut accensum ardeat donec totum consumatur, nihilque fæcum aut phlegmatis in fundo remaneat. The words meaning became restricted to spirit of wine in the 18th century and was extended to the class of substances so-called as alcohols in modern chemistry after 1850, the term ethanol was invented 1892, based on combining the word ethane with ol the last part of alcohol. In the IUPAC system, in naming simple alcohols, the name of the alkane chain loses the terminal e and adds ol, e. g. as in methanol and ethanol. When necessary, the position of the group is indicated by a number between the alkane name and the ol, propan-1-ol for CH 3CH 2CH 2OH, propan-2-ol for CH 3CHCH3. If a higher priority group is present, then the prefix hydroxy is used, in other less formal contexts, an alcohol is often called with the name of the corresponding alkyl group followed by the word alcohol, e. g. methyl alcohol, ethyl alcohol. Propyl alcohol may be n-propyl alcohol or isopropyl alcohol, depending on whether the group is bonded to the end or middle carbon on the straight propane chain. As described under systematic naming, if another group on the molecule takes priority, Alcohols are then classified into primary, secondary, and tertiary, based upon the number of carbon atoms connected to the carbon atom that bears the hydroxyl functional group. The primary alcohols have general formulas RCH2OH, the simplest primary alcohol is methanol, for which R=H, and the next is ethanol, for which R=CH3, the methyl group. Secondary alcohols are those of the form RRCHOH, the simplest of which is 2-propanol, for the tertiary alcohols the general form is RRRCOH
21.
Nitrogen
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Nitrogen is a chemical element with symbol N and atomic number 7. It was first discovered and isolated by Scottish physician Daniel Rutherford in 1772, although Carl Wilhelm Scheele and Henry Cavendish had independently done so at about the same time, Rutherford is generally accorded the credit because his work was published first. Nitrogen is the lightest member of group 15 of the periodic table, the name comes from the Greek πνίγειν to choke, directly referencing nitrogens asphyxiating properties. It is an element in the universe, estimated at about seventh in total abundance in the Milky Way. At standard temperature and pressure, two atoms of the element bind to form dinitrogen, a colourless and odorless diatomic gas with the formula N2, dinitrogen forms about 78% of Earths atmosphere, making it the most abundant uncombined element. Nitrogen occurs in all organisms, primarily in amino acids, in the nucleic acids, the human body contains about 3% nitrogen by mass, the fourth most abundant element in the body after oxygen, carbon, and hydrogen. The nitrogen cycle describes movement of the element from the air, into the biosphere and organic compounds, many industrially important compounds, such as ammonia, nitric acid, organic nitrates, and cyanides, contain nitrogen. The extremely strong bond in elemental nitrogen, the second strongest bond in any diatomic molecule. Synthetically produced ammonia and nitrates are key industrial fertilisers, and fertiliser nitrates are key pollutants in the eutrophication of water systems. Apart from its use in fertilisers and energy-stores, nitrogen is a constituent of organic compounds as diverse as Kevlar used in high-strength fabric, Nitrogen is a constituent of every major pharmacological drug class, including antibiotics. Many notable nitrogen-containing drugs, such as the caffeine and morphine or the synthetic amphetamines. Nitrogen compounds have a long history, ammonium chloride having been known to Herodotus. They were well known by the Middle Ages, alchemists knew nitric acid as aqua fortis, as well as other nitrogen compounds such as ammonium salts and nitrate salts. The mixture of nitric and hydrochloric acids was known as aqua regia, celebrated for its ability to dissolve gold, the discovery of nitrogen is attributed to the Scottish physician Daniel Rutherford in 1772, who called it noxious air. Though he did not recognise it as a different chemical substance, he clearly distinguished it from Joseph Blacks fixed air. The fact that there was a component of air that does not support combustion was clear to Rutherford, Nitrogen was also studied at about the same time by Carl Wilhelm Scheele, Henry Cavendish, and Joseph Priestley, who referred to it as burnt air or phlogisticated air. Nitrogen gas was inert enough that Antoine Lavoisier referred to it as air or azote, from the Greek word άζωτικός. In an atmosphere of nitrogen, animals died and flames were extinguished
22.
Chemical polarity
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In chemistry, polarity is a separation of electric charge leading to a molecule or its chemical groups having an electric dipole or multipole moment. Polar molecules must contain polar bonds due to a difference in electronegativity between the bonded atoms, a polar molecule with two or more polar bonds must have an asymmetric geometry so that the bond dipoles do not cancel each other. Polar molecules interact through dipole–dipole intermolecular forces and hydrogen bonds, Polarity underlies a number of physical properties including surface tension, solubility, and melting and boiling points. Not all atoms attract electrons with the same force, the amount of pull an atom exerts on its electrons is called its electronegativity. Atoms with high electronegativities – such as fluorine, oxygen and nitrogen – exert a pull on electrons than atoms with lower electronegativities. In a bond, this leads to sharing of electrons between the atoms, as electrons will be drawn closer to the atom with the higher electronegativity. Because electrons have a charge, the unequal sharing of electrons within a bond leads to the formation of an electric dipole. Because the amount of charge separated in such dipoles is usually smaller than a charge, they are called partial charges, denoted as δ+. These symbols were introduced by Christopher Kelk Ingold and Edith Hilda Ingold in 1926, the bond dipole moment is calculated by multiplying the amount of charge separated and the distance between the charges. These dipoles within molecules can interact with dipoles in other molecules, Bonds can fall between one of two extremes – being completely nonpolar or completely polar. A completely nonpolar bond occurs when the electronegativities are identical and therefore possess a difference of zero, a completely polar bond is more correctly called an ionic bond, and occurs when the difference between electronegativities is large enough that one atom actually takes an electron from the other. The terms polar and nonpolar are usually applied to covalent bonds, to determine the polarity of a covalent bond using numerical means, the difference between the electronegativity of the atoms is used. Bond polarity is typically divided into three groups that are based on the difference in electronegativity between the two bonded atoms. He estimated that a difference of 1.7 corresponds to 50% ionic character, see also dipole § Molecular dipoles. While the molecules can be described as covalent, nonpolar covalent, or ionic. However, the properties are typical of such molecules. A molecule is composed of one or more chemical bonds between molecular orbitals of different atoms, a polar molecule has a net dipole as a result of the opposing charges from polar bonds arranged asymmetrically. Water is an example of a polar molecule since it has a positive charge on one side
23.
Acetoxy group
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Acetoxy group, abbreviated AcO or OAc, is a chemical functional group of the structure CH3-C-O-. It differs from the acetyl group CH3-C- by the presence of one oxygen atom. The name acetoxy is the form of acetyl-oxy. An acetoxy group may be used as a protection for an alcohol functionality in a synthetic route although the group itself is called an acetyl group. Acetic anhydride in the presence of base with a catalyst such as pyridine with a bit of DMAP added, an alcohol is not a particularly strong nucleophile and, when present, more powerful nucleophiles like amines will react with the above-mentioned reagents in preference to the alcohol. For deprotection Aqueous base Aqueous acid, may have to be heated Anhydrous base such as sodium methoxide in methanol, very useful when a methyl ester of a carboxylic acid is also present in the molecule, as it will not hydrolyze it like an aqueous base would
24.
Methoxy group
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In chemistry, methoxy refers to the functional group consisting of a methyl group bound to oxygen. This alkoxy group has the formula O–CH3, the term is used in organic chemistry usually to describe an ether. As quantified by the Hammett equation, methoxy is an electron-donating group, the simplest methoxy compounds are methanol and dimethyl ether. Other methoxy ethers include anisole and vanillin, many metal alkoxides contain methoxy groups, e. g. tetramethyl orthosilicate and titanium methoxide. Such compounds are classified as methoxides. In nature, methoxy groups are found on nucleosides that have been subjected to 2-O-methylation, for example in variations of the 5-cap structure known as cap-1 and cap-2. They are also common substituents in O-methylated flavonoids, whose formation is catalyzed by O-methyltransferases that act on phenols, a large number of natural products in plants, e. g. lignins, are generated via catalysis by caffeoyl-CoA O-methyltransferase. Commonly organic methoxides are derived by methylation of alkoxides, some aryl methoxides are available via metal-catalyzed methylation of phenols, or as well methoxylation of aromatic halogenides
25.
Pyrolysis
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Pyrolysis is a thermochemical decomposition of organic material at elevated temperatures in the absence of oxygen. It involves the change of chemical composition and physical phase. The word is coined from the Greek-derived elements pyro fire and lysis separating, Pyrolysis is a type of thermolysis, and is most commonly observed in organic materials exposed to high temperatures. It is one of the involved in charring wood, starting at 200–300 °C. It also occurs in fires where solid fuels are burning or when vegetation comes into contact with lava in volcanic eruptions, in general, pyrolysis of organic substances produces gas and liquid products and leaves a solid residue richer in carbon content, char. Extreme pyrolysis, which leaves mostly carbon as the residue, is called carbonization and these specialized uses of pyrolysis may be called various names, such as dry distillation, destructive distillation, or cracking. Pyrolysis is also used in the creation of nanoparticles, zirconia, Pyrolysis also plays an important role in several cooking procedures, such as baking, frying, grilling, and caramelizing. It is a tool of analysis, for example, in mass spectrometry. Indeed, many important chemical substances, such as phosphorus and sulfuric acid, were first obtained by this process, Pyrolysis has been assumed to take place during catagenesis, the conversion of buried organic matter to fossil fuels. It is also the basis of pyrography, in their embalming process, the ancient Egyptians used a mixture of substances, including methanol, which they obtained from the pyrolysis of wood. Pyrolysis differs from other processes like combustion and hydrolysis in that it usually does not involve reactions with oxygen, water, in practice, it is not possible to achieve a completely oxygen-free atmosphere. Because some oxygen is present in any system, a small amount of oxidation occurs. The term has also applied to the decomposition of organic material in the presence of superheated water or steam, for example. Pyrolysis is usually the first chemical reaction occurs in the burning of many solid organic fuels, like wood, cloth, and paper. Thus, the pyrolysis of common materials like wood, plastic, in pyrolysis there is a gas phase present. Pyrolysis occurs whenever food is exposed to high temperatures in a dry environment, such as roasting, baking, toasting. It is the process responsible for the formation of the golden-brown crust in foods prepared by those methods. In normal cooking, the food components that undergo pyrolysis are carbohydrates
26.
Sodium channel
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Sodium channels are integral membrane proteins that form ion channels, conducting sodium ions through a cells plasma membrane. They are classified according to the trigger that opens the channel for such ions, in excitable cells such as neurons, myocytes, and certain types of glia, sodium channels are responsible for the rising phase of action potentials. These channels go through 3 different states called as resting, active and inactive states, even though the resting and inactive states wouldnt allow the ions to flow through the channels the difference exists with respect to their structural conformation. Sodium channels are selective for the transport of sodium ions across cell membranes. The high selectivity with respect to the ion is achieved in many different ways. All involve encapsulation of the ion in a cavity of specific size within a larger molecule. Sodium channels consist of large α subunits that associate with proteins, an α subunit forms the core of the channel and is functional on its own. When the α subunit protein is expressed by a cell, it is able to form channels that conduct Na+ in a voltage-gated way, when accessory proteins assemble with α subunits, the resulting complex can display altered voltage dependence and cellular localization. The α-subunit has four domains, labeled I through IV, each containing six membrane-spanning segments. The highly conserved S4 segment acts as the voltage sensor. The voltage sensitivity of this channel is due to amino acids located at every third position. When stimulated by a change in voltage, this segment moves toward the extracellular side of the cell membrane. The ions are conducted through a pore, which can be broken into two regions, the more external portion of the pore is formed by the P-loops of the four domains. This region is the most narrow part of the pore and is responsible for its ion selectivity, the inner portion of the pore is formed by the combined S5 and S6 segments of the four domains. The region linking domains III and IV is also important for channel function and this region plugs the channel after prolonged activation, inactivating it. Voltage-gated Na+ channels have three main states, closed, open and inactivated. Forward/back transitions between states are correspondingly referred to as activation/deactivation, inactivation/reactivation, and recovery from inactivation/closed-state inactivation. Closed and inactivated states are ion impermeable, because the voltage across the membrane is initially negative, as its voltage increases to and past zero, it is said to depolarize
27.
Depolarization
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In biology, depolarization is a change within a cell, during which the cell undergoes a shift in electric charge distribution, resulting in less negative charge inside the cell. Depolarization is essential to the function of cells, communication between cells, and the overall physiology of an organism. Most cells in higher organisms maintain an environment that is negatively charged relative to the cells exterior. This difference in charge is called the membrane potential. In the process of depolarization, the internal charge of the cell temporarily becomes more positive. This shift from a negative to a more positive membrane potential occurs during several processes, during an action potential, the depolarization is so large that the potential difference across the cell membrane briefly reverses polarity, with the inside of the cell becoming positively charged. The change in charge typically occurs due to an influx of ions into a cell. The opposite of a depolarization is called a hyperpolarization, usage of the term depolarization in biology differs from its use in physics. In physics it refers instead to situations in which any form of polarity changes to a value of zero, the process of depolarization is entirely dependent upon the intrinsic electrical nature of most cells. When a cell is at rest, the cell maintains what is known as a resting potential, the resting potential generated by nearly all cells results in the interior of the cell having a negative charge compared to the exterior of the cell. To maintain this electrical imbalance, microscopic positively and negatively charged particles called ions are transported across the plasma membrane. The resting potential must be established within a cell before the cell can be depolarized, there are many mechanisms by which a cell can establish a resting potential, however there is a typical pattern of generating this resting potential that many cells follow. The cell uses ion channels, ion pumps, and voltage gated ion channels to generate a negative resting potential within the cell, however, the process of generating the resting potential within the cell also creates an environment outside of the cell that favors depolarization. The sodium potassium pump is largely responsible for the optimization of conditions on both the interior and the exterior of the cell for depolarization, additionally, despite the high concentration of positively-charged potassium ions, most cells contain internal components, which accumulate to establish a negative inner-charge. After a cell has established a potential, that cell has the capacity to undergo depolarization. During depolarization, the charge within the cell rapidly shifts from negative to positive, for this rapid change to take place within the interior of the cell, several events must occur along the plasma membrane of the cell as well. While the sodium potassium pump continues to work, the voltage gated ion channels that had closed while the cell was at resting potential have been opened by an electrical stimulus. As the sodium rushes back into the cell the positive sodium ions raise the charge inside the cell from negative to positive, once the interior of the cell becomes positively charged, depolarization of the cell is complete
28.
Receptor (biochemistry)
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In biochemistry and pharmacology, a receptor is a protein molecule that receives chemical signals from outside a cell. When such chemical signals bind to a receptor, they cause some form of cellular/tissue response, however, sometimes in pharmacology, the term is also used to include other proteins that are drug targets, such as enzymes, transporters and ion channels. Receptor proteins can be classified by their location, transmembrane receptors include ion channel-linked receptors, G protein-linked hormone receptors, and enzyme-linked hormone receptors. Intracellular receptors are found inside the cell, and include cytoplasmic receptors. The endogenously designated -molecule for a receptor is referred to as its endogenous ligand. E. g. the endogenous ligand for the acetylcholine receptor is acetylcholine but the receptor can also be activated by nicotine. Each receptor is linked to a specific cellular biochemical pathway, while numerous receptors are found in most cells, each receptor will only bind with ligands of a particular structure, much like how locks will only accept specifically shaped keys. When a ligand binds to its receptor, it activates or inhibits the receptors associated biochemical pathway. The ligand-binding cavities are located at the interface between the subunits, type 2, G protein-coupled receptors – This is the largest family of receptors and includes the receptors for several hormones and slow transmitters e. g. dopamine, metabotropic glutamate. They are composed of seven transmembrane alpha helices, the loops connecting the alpha helices form extracellular and intracellular domains. The aforementioned receptors are coupled to different intracellular effector systems via G proteins, the insulin receptor is an example. Type 4, Nuclear receptors – While they are called nuclear receptors, they are located in the cytoplasm. They are composed of a C-terminal ligand-binding region, a core DNA-binding domain, the core region has two zinc fingers that are responsible for recognizing the DNA sequences specific to this receptor. The N terminus interacts with other transcription factors in a ligand-independent manner. Steroid and thyroid-hormone receptors are examples of such receptors, membrane receptors may be isolated from cell membranes by complex extraction procedures using solvents, detergents, and/or affinity purification. The structures and actions of receptors may be studied by using methods such as X-ray crystallography, NMR, circular dichroism. Computer simulations of the behavior of receptors have been used to gain understanding of their mechanisms of action. Ligand binding is an equilibrium process, ligands bind to receptors and dissociate from them according to the law of mass action
29.
Acetylcholine receptor
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An acetylcholine receptor is an integral membrane protein that responds to the binding of acetylcholine, a neurotransmitter. Like other transmembrane receptors, acetylcholine receptors are classified according to their pharmacology, although all acetylcholine receptors, by definition, respond to acetylcholine, they respond to other molecules as well. Nicotinic acetylcholine receptors are particularly responsive to nicotine, the nicotine ACh receptor is also a Na+, K+ and Ca2+ ion channel. Muscarinic acetylcholine receptors are particularly responsive to muscarine, nicotinic and muscarinic are two main kinds of cholinergic receptors. Molecular biology has shown that the nicotinic and muscarinic receptors belong to distinct protein superfamilies, nicotinic receptors are of two types, Nm and Nn. Nm is located in the junction which causes the contraction of skeletal muscles by way of end-plate potential. Nn causes depolarization in autonomic ganglia resulting in post ganglionic impulse, nicotinic receptors cause the release of catecholamine from the adrenal medulla, and also site specific excitation or inhibition in brain. Both Nm and Nn are Na+ and Ca++ channel linked but Nn is also linked with an extra K+ channel, the subunit composition is highly variable across different tissues. Each subunit contains four regions which span the membrane and consist of approximately 20 amino acids, region II which sits closest to the pore lumen, forms the pore lining. Binding of acetylcholine to the N termini of each of the two alpha subunits results in the 15° rotation of all M2 helices. In the intermediate region of the receptor, within the pore lumen, the nAChR is found at the edges of junctional folds at the neuromuscular junction on the postsynaptic side, it is activated by acetylcholine release across the synapse. In contrast, the mAChRs are not ion channels, but belong instead to the superfamily of G-protein-coupled receptors that activate other ionic channels via a second messenger cascade, the muscarine cholinergic receptor activates a G-protein when bound to extracellular ACh. The alpha subunit of the G-protein deactivates adenylate cyclase while the beta-gamma subunit activates the K-channels and this causes a decrease in cardiac activity. Nicotinic acetylcholine receptors can be blocked by curare, hexamethonium and toxins present in the venoms of snakes and shellfishes, drugs such as the neuromuscular blocking agents bind reversibly to the nicotinic receptors in the neuromuscular junction and are used routinely in anaesthesia. Nicotinic receptors are the primary mediator of the effects of nicotine, in myasthenia gravis, the receptor at the neuromuscular junction is targeted by antibodies, leading to muscle weakness. Muscarinic acetylcholine receptors can be blocked by the drugs atropine and scopolamine, congenital myasthenic syndrome is an inherited neuromuscular disorder caused by defects of several types at the neuromuscular junction. Postsynaptic defects are the most frequent cause of CMS and often result in abnormalities in nicotinic acetylcholine receptors, the majority of mutations causing CMS are found in the AChR subunits genes. Out of all associated with CMS, more than half are mutations in one of the four genes encoding the adult acetylcholine receptor subunits
30.
Chemical synapse
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Chemical synapses are biological junctions through which neurons signals can be exchanged to each other and to non-neuronal cells such as those in muscles or glands. Chemical synapses allow neurons to form circuits within the nervous system. They are crucial to the computations that underlie perception and thought. They allow the system to connect to and control other systems of the body. At a chemical synapse, one neuron releases neurotransmitter molecules into a space that is adjacent to another neuron. The neurotransmitters are kept within small sacs called vesicles, and are released into the synaptic cleft by exocytosis and these molecules then bind to receptors on the postsynaptic cells side of the synaptic cleft. The adult human brain is estimated to contain from 1014 to 5 ×1014 synapses, every cubic millimeter of cerebral cortex contains roughly a billion of them. The word synapse comes from synaptein, which Sir Charles Scott Sherrington and colleagues coined from the Greek syn-, chemical synapses are not the only type of biological synapse, electrical and immunological synapses also exist. Without a qualifier, however, synapse commonly means chemical synapse, synapses are functional connections between neurons, or between neurons and other types of cells. A typical neuron gives rise to several thousand synapses, although there are types that make far fewer. Most synapses connect axons to dendrites, but there are other types of connections, including axon-to-cell-body, axon-to-axon. Chemical synapses pass information directionally from a cell to a postsynaptic cell and are therefore asymmetric in structure. Synaptic vesicles are docked at the plasma membrane at regions called active zones. Immediately opposite is a region of the cell containing neurotransmitter receptors. Immediately behind the postsynaptic membrane is a complex of interlinked proteins called the postsynaptic density. Proteins in the PSD are involved in anchoring and trafficking neurotransmitter receptors, the receptors and PSDs are often found in specialized protrusions from the main dendritic shaft called dendritic spines. Synapses may be described as symmetric or asymmetric, when examined under an electron microscope, asymmetric synapses are characterized by rounded vesicles in the presynaptic cell, and a prominent postsynaptic density. Symmetric synapses in contrast have flattened or elongated vesicles, and do not contain a prominent postsynaptic density, the synaptic cleft is a gap between the pre- and postsynaptic cells that is about 20 nm wide
31.
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
32.
Terpenoid
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Most are multicyclic structures that differ from one another not only in functional groups but also in their basic carbon skeletons. These lipids can be found in all classes of living things, about 60% of known natural products are terpenoids. Plant terpenoids are used extensively for their qualities and play a role in traditional herbal remedies. Terpenoids contribute to the scent of eucalyptus, the flavors of cinnamon, cloves, and ginger, the color in sunflowers. The steroids and sterols in animals are produced from terpenoid precursors. Sometimes terpenoids are added to proteins, e. g. to enhance their attachment to the cell membrane, terpenes are hydrocarbons resulting from the condensation of several 5-carbon isoprene units. The isoprene unit has the formula CH2=CCH=CH2, terpenoids can be thought of as modified terpenes, wherein methyl groups have been moved or removed, or oxygen atoms added. The Salkowski test can be used to identify the presence of terpenoids, meroterpenes are any compound, including many natural products, having a partial terpenoid structure. There are two pathways that create terpenoids, Many organisms manufacture terpenoids through the HMG-CoA reductase pathway. The reactions take place in the cytosol, the pathway was discovered in the 1950s. It was discovered in the late 1980s, pyruvate and glyceraldehyde 3-phosphate are converted by DOXP synthase to 1-deoxy-D-xylulose 5-phosphate, and by DOXP reductase to 2-C-methyl-D-erythritol 4-phosphate. IPP and DMAPP are the end-products in either pathway, and are the precursors of isoprene, monoterpenoids, diterpenoids, carotenoids, chlorophylls, synthesis of all higher terpenoids proceeds via formation of geranyl pyrophosphate, farnesyl pyrophosphate, and geranylgeranyl pyrophosphate. Although both pathways, MVA and MEP, are exclusive in most organisms, interactions between them have been reported in plants and few bacteria species. It is a material for synthesis of vitamin A. List of antioxidants in food List of phytochemicals in food Nutrition Phytochemistry Secondary metabolites IUPAC nomenclature of terpenoids
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Aldehyde
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The group—without R—is the aldehyde group, also known as the formyl group. Aldehydes are common in organic chemistry, Aldehydes feature an sp2-hybridized, planar carbon center that is connected by a double bond to oxygen and a single bond to hydrogen. The C–H bond is not ordinarily acidic, because of resonance stabilization of the conjugate base, an α-hydrogen in an aldehyde is far more acidic, with a pKa near 15, compared to the acidity of a typical alkane. This acidification is attributed to the quality of the formyl center and the fact that the conjugate base. Related to, the group is somewhat polar. Aldehydes can exist in either the keto or the enol tautomer, keto-enol tautomerism is catalyzed by either acid or base. Usually the enol is the minority tautomer, but it is more reactive, the common names for aldehydes do not strictly follow official guidelines, such as those recommended by IUPAC, but these rules are useful. IUPAC prescribes the following nomenclature for aldehydes, Acyclic aliphatic aldehydes are named as derivatives of the longest carbon chain containing the aldehyde group, thus, HCHO is named as a derivative of methane, and CH3CH2CH2CHO is named as a derivative of butane. The name is formed by changing the suffix -e of the parent alkane to -al, so that HCHO is named methanal, in other cases, such as when a -CHO group is attached to a ring, the suffix -carbaldehyde may be used. Thus, C6H11CHO is known as cyclohexanecarbaldehyde, if the presence of another functional group demands the use of a suffix, the aldehyde group is named with the prefix formyl-. This prefix is preferred to methanoyl-, the word aldehyde was coined by Justus von Liebig as a contraction of the Latin alcohol dehydrogenatus. In the past, aldehydes were sometimes named after the corresponding alcohols, for example, the term formyl group is derived from the Latin word formica ant. This word can be recognized in the simplest aldehyde, formaldehyde, Aldehydes have properties that are diverse and that depend on the remainder of the molecule. Smaller aldehydes are more soluble in water, formaldehyde and acetaldehyde completely so, the volatile aldehydes have pungent odors. Aldehydes degrade in air via the process of autoxidation, the two aldehydes of greatest importance in industry, formaldehyde and acetaldehyde, have complicated behavior because of their tendency to oligomerize or polymerize. They also tend to hydrate, forming the geminal diol, the oligomers/polymers and the hydrates exist in equilibrium with the parent aldehyde. Aldehydes are readily identified by spectroscopic methods, using IR spectroscopy, they display a strong νCO band near 1700 cm−1. In their 1H NMR spectra, the formyl hydrogen center absorbs near δH =9 and this signal shows the characteristic coupling to any protons on the alpha carbon
34.
Lactone
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Lactones are cyclic esters of hydroxycarboxylic acids, containing a 1-oxacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. Lactones are formed by esterification of the corresponding hydroxycarboxylic acids. Lactones with three- or four-membered rings are very reactive, making their isolation difficult, special methods are normally required for the laboratory synthesis of small-ring lactones as well as those that contain rings larger than six-membered. The first carbon atom after the carbon in the group on the parent compound is labelled α, the second will be labeled β. Therefore, the prefixes also indicate the size of the ring, α-lactone = 3-membered ring, β-lactone = 4-membered, γ-lactone = 5-membered. The other suffix used to denote a lactone is -olide, used in substance class names like butenolide, macrolide, cardenolide or bufadienolide, the name lactone derives from the ring compound called lactide, which is formed from the dehydration of 2-hydroxypropanoic acid CH3-CH-COOH. Lactic acid, in turn, derives its name from its isolation from soured milk. An internal dehydration within the molecule of lactic acid would have produced alpha-propiolactone. Naturally occurring lactones are mainly saturated and unsaturated γ- and δ-lactones, the γ- and δ-lactones are intramolecular esters of the corresponding hydroxy fatty acids. They contribute to the aroma of butter, cheese and various foods, cyclopentadecanolide is responsible for the musklike odor of angelica root oil. Of the naturally occurring bicyclic lactones, phthalides are responsible for the odors of celery and lovage oils, many methods in ester synthesis can also be applied to that of lactones. In one industrial synthesis of oxandrolone the key lactone-forming step is an organic reduction - esterification, in halolactonization, an alkene is attacked by a halogen via electrophilic addition with the cationic intermediate captured intramolecularly by an adjacent carboxylic acid. Specific methods include Yamaguchi esterification, Shiina macrolactonization, Baeyer–Villiger oxidation, the most stable structure for lactones are the 5-membered γ-lactones and 6-membered δ-lactones because, as in all organic cycles,5 and 6 membered rings minimize the strain of bond angles. γ-lactones are so stable that, in the presence of acids at room temperature. β-lactones do exist, but can only be made by special methods, α-lactones can be detected as transient species in mass spectrometry experiments. Like straight-chained esters, the reaction of lactones is a reversible reaction. However, the constant of the hydrolysis reaction of the lactone is lower than that of the straight-chained ester i. e. the products are less favored in the case of the lactones. This is because although the enthalpies of the hydrolysis of esters and lactones are about the same, straight-chained esters give two products upon hydrolysis, making the entropy change more favorable than in the case of lactones which give only a single product
35.
Aldol condensation
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Aldol condensations are important in organic synthesis, because they provide a good way to form carbon–carbon bonds. For example, the Robinson annulation reaction sequence features an aldol condensation, aldol condensations are also commonly discussed in university level organic chemistry classes as a good bond-forming reaction that demonstrates important reaction mechanisms. The name aldol condensation is also used, especially in biochemistry. However, the reaction is not formally a condensation reaction because it does not involve the loss of a small molecule. The reaction between an aldehyde/ketone and a carbonyl compound lacking an alpha-hydrogen is called the Claisen-Schmidt condensation. This reaction is named after two of its pioneering investigators Rainer Ludwig Claisen and J. G. Schmidt, who published on this topic in 1880 and 1881. An example is the synthesis of dibenzylideneacetone, quantitative yields in Claisen-Schmidt reactions have been reported in the absence of solvent using sodium hydroxide as the base and plus benzaldehydes. The first part of reaction is an aldol reaction, the second part a dehydration—an elimination reaction. Dehydration may be accompanied by decarboxylation when an activated carboxyl group is present, depending on the nature of the desired product, the aldol condensation may be carried out under two broad types of conditions, kinetic control or thermodynamic control. It is important to distinguish the aldol condensation from other reactions of carbonyl compounds. When the base is an amine and the active compound is sufficiently activated the reaction is called a Knoevenagel condensation. In a Perkin reaction the aldehyde is aromatic and the enolate generated from an anhydride, a Claisen condensation involves two ester compounds. A Dieckmann condensation involves two groups in the same molecule and yields a cyclic molecule A Henry reaction involves an aldehyde. A Robinson annulation involves a α, β-unsaturated ketone and a carbonyl group, in the Guerbet reaction, an aldehyde, formed in situ from an alcohol, self-condenses to the dimerized alcohol. The synthetic procedure is typical for this type of reaction, in the process, in addition to water, an equivalent of ethanol and carbon dioxide are lost in decarboxylation. Ethyl glyoxylate 2 and diethyl 2-methylglutaconate 1 react to isoprenetricarboxylic acid 3 with sodium ethoxide and this reaction product is very unstable with initial loss of carbon dioxide and followed by many secondary reactions. This is believed to be due to strain resulting from the methyl group. Support for the mechanism is based on isotope labeling
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