1.
Jmol
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Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool and it is written in the programming language Java, so it can run on the operating systems Windows, macOS, Linux, and Unix, if Java is installed. It is free and open-source software released under a GNU Lesser General Public License version 2.0, a standalone application and a software development kit exist that can be integrated into other Java applications, such as Bioclipse and Taverna. A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways, for example, molecules can be displayed as ball-and-stick models, space-filling models, ribbon diagrams, etc. Jmol supports a range of chemical file formats, including Protein Data Bank, Crystallographic Information File, MDL Molfile. There is also a JavaScript-only version, JSmol, that can be used on computers with no Java, the Jmol applet, among other abilities, offers an alternative to the Chime plug-in, which is no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS9. Jmol requires Java installation and operates on a variety of platforms. For example, Jmol is fully functional in Mozilla Firefox, Internet Explorer, Opera, Google Chrome, fast and Scriptable Molecular Graphics in Web Browsers without Java3D
2.
ChemSpider
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ChemSpider is a database of chemicals. ChemSpider is owned by the Royal Society of Chemistry, the database contains information on more than 50 million molecules from over 500 data sources including, Each chemical is given a unique identifier, which forms part of a corresponding URL. This is an approach to develop an online chemistry database. The search can be used to widen or restrict already found results, structure searching on mobile devices can be done using free apps for iOS and for the Android. The ChemSpider database has been used in combination with text mining as the basis of document markup. The result is a system between chemistry documents and information look-up via ChemSpider into over 150 data sources. ChemSpider was acquired by the Royal Society of Chemistry in May,2009, prior to the acquisition by RSC, ChemSpider was controlled by a private corporation, ChemZoo Inc. The system was first launched in March 2007 in a release form. ChemSpider has expanded the generic support of a database to include support of the Wikipedia chemical structure collection via their WiChempedia implementation. A number of services are available online. SyntheticPages is an interactive database of synthetic chemistry procedures operated by the Royal Society of Chemistry. Users submit synthetic procedures which they have conducted themselves for publication on the site and these procedures may be original works, but they are more often based on literature reactions. Citations to the published procedure are made where appropriate. They are checked by an editor before posting. The pages do not undergo formal peer-review like a journal article. The comments are moderated by scientific editors. The intention is to collect practical experience of how to conduct useful chemical synthesis in the lab, while experimental methods published in an ordinary academic journal are listed formally and concisely, the procedures in ChemSpider SyntheticPages are given with more practical detail. Comments by submitters are included as well, other publications with comparable amounts of detail include Organic Syntheses and Inorganic Syntheses
3.
European Chemicals Agency
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ECHA is the driving force among regulatory authorities in implementing the EUs chemicals legislation. ECHA helps companies to comply with the legislation, advances the safe use of chemicals, provides information on chemicals and it is located in Helsinki, Finland. The Agency, headed by Executive Director Geert Dancet, started working on 1 June 2007, the REACH Regulation requires companies to provide information on the hazards, risks and safe use of chemical substances that they manufacture or import. Companies register this information with ECHA and it is freely available on their website. So far, thousands of the most hazardous and the most commonly used substances have been registered, the information is technical but gives detail on the impact of each chemical on people and the environment. This also gives European consumers the right to ask whether the goods they buy contain dangerous substances. The Classification, Labelling and Packaging Regulation introduces a globally harmonised system for classifying and labelling chemicals into the EU. This worldwide system makes it easier for workers and consumers to know the effects of chemicals, companies need to notify ECHA of the classification and labelling of their chemicals. So far, ECHA has received over 5 million notifications for more than 100000 substances, the information is freely available on their website. Consumers can check chemicals in the products they use, Biocidal products include, for example, insect repellents and disinfectants used in hospitals. The Biocidal Products Regulation ensures that there is information about these products so that consumers can use them safely. ECHA is responsible for implementing the regulation, the law on Prior Informed Consent sets guidelines for the export and import of hazardous chemicals. Through this mechanism, countries due to hazardous chemicals are informed in advance and have the possibility of rejecting their import. Substances that may have effects on human health and the environment are identified as Substances of Very High Concern 1. These are mainly substances which cause cancer, mutation or are toxic to reproduction as well as substances which persist in the body or the environment, other substances considered as SVHCs include, for example, endocrine disrupting chemicals. Companies manufacturing or importing articles containing these substances in a concentration above 0 and they are required to inform users about the presence of the substance and therefore how to use it safely. Consumers have the right to ask the retailer whether these substances are present in the products they buy, once a substance has been officially identified in the EU as being of very high concern, it will be added to a list. This list is available on ECHA’s website and shows consumers and industry which chemicals are identified as SVHCs, Substances placed on the Candidate List can then move to another list
4.
PubChem
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PubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information, a component of the National Library of Medicine, PubChem can be accessed for free through a web user interface. Millions of compound structures and descriptive datasets can be downloaded via FTP. PubChem contains substance descriptions and small molecules with fewer than 1000 atoms and 1000 bonds, more than 80 database vendors contribute to the growing PubChem database. PubChem consists of three dynamically growing primary databases, as of 28 January 2016, Compounds,82.6 million entries, contains pure and characterized chemical compounds. Substances,198 million entries, contains also mixtures, extracts, complexes, bioAssay, bioactivity results from 1.1 million high-throughput screening programs with several million values. PubChem contains its own online molecule editor with SMILES/SMARTS and InChI support that allows the import and export of all common chemical file formats to search for structures and fragments. In the text search form the database fields can be searched by adding the name in square brackets to the search term. A numeric range is represented by two separated by a colon. The search terms and field names are case-insensitive, parentheses and the logical operators AND, OR, and NOT can be used. AND is assumed if no operator is used, example,0,5000,50,10 -5,5 PubChem was released in 2004. The American Chemical Society has raised concerns about the publicly supported PubChem database and they have a strong interest in the issue since the Chemical Abstracts Service generates a large percentage of the societys revenue. To advocate their position against the PubChem database, ACS has actively lobbied the US Congress, soon after PubChems creation, the American Chemical Society lobbied U. S. Congress to restrict the operation of PubChem, which they asserted competes with their Chemical Abstracts Service
5.
International Chemical Identifier
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Initially developed by IUPAC and NIST from 2000 to 2005, the format and algorithms are non-proprietary. The continuing development of the standard has supported since 2010 by the not-for-profit InChI Trust. The current version is 1.04 and was released in September 2011, prior to 1.04, the software was freely available under the open source LGPL license, but it now uses a custom license called IUPAC-InChI Trust License. Not all layers have to be provided, for instance, the layer can be omitted if that type of information is not relevant to the particular application. InChIs can thus be seen as akin to a general and extremely formalized version of IUPAC names and they can express more information than the simpler SMILES notation and differ in that every structure has a unique InChI string, which is important in database applications. Information about the 3-dimensional coordinates of atoms is not represented in InChI, the InChI algorithm converts input structural information into a unique InChI identifier in a three-step process, normalization, canonicalization, and serialization. The InChIKey, sometimes referred to as a hashed InChI, is a fixed length condensed digital representation of the InChI that is not human-understandable. The InChIKey specification was released in September 2007 in order to facilitate web searches for chemical compounds and it should be noted that, unlike the InChI, the InChIKey is not unique, though collisions can be calculated to be very rare, they happen. In January 2009 the final 1.02 version of the InChI software was released and this provided a means to generate so called standard InChI, which does not allow for user selectable options in dealing with the stereochemistry and tautomeric layers of the InChI string. The standard InChIKey is then the hashed version of the standard InChI string, the standard InChI will simplify comparison of InChI strings and keys generated by different groups, and subsequently accessed via diverse sources such as databases and web resources. Every InChI starts with the string InChI= followed by the version number and this is followed by the letter S for standard InChIs. The remaining information is structured as a sequence of layers and sub-layers, the layers and sub-layers are separated by the delimiter / and start with a characteristic prefix letter. The six layers with important sublayers are, Main layer Chemical formula and this is the only sublayer that must occur in every InChI. The atoms in the formula are numbered in sequence, this sublayer describes which atoms are connected by bonds to which other ones. Describes how many hydrogen atoms are connected to each of the other atoms, the condensed,27 character standard InChIKey is a hashed version of the full standard InChI, designed to allow for easy web searches of chemical compounds. Most chemical structures on the Web up to 2007 have been represented as GIF files, the full InChI turned out to be too lengthy for easy searching, and therefore the InChIKey was developed. With all databases currently having below 50 million structures, such duplication appears unlikely at present, a recent study more extensively studies the collision rate finding that the experimental collision rate is in agreement with the theoretical expectations. Example, Morphine has the structure shown on the right, as the InChI cannot be reconstructed from the InChIKey, an InChIKey always needs to be linked to the original InChI to get back to the original structure
6.
Simplified molecular-input line-entry system
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The simplified molecular-input line-entry system is a specification in form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules, the original SMILES specification was initiated in the 1980s. It has since modified and extended. In 2007, a standard called OpenSMILES was developed in the open-source chemistry community. Other linear notations include the Wiswesser Line Notation, ROSDAL and SLN, the original SMILES specification was initiated by David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s. The Environmental Protection Agency funded the project to develop SMILES. It has since modified and extended by others, most notably by Daylight Chemical Information Systems. In 2007, a standard called OpenSMILES was developed by the Blue Obelisk open-source chemistry community. Other linear notations include the Wiswesser Line Notation, ROSDAL and SLN, in July 2006, the IUPAC introduced the InChI as a standard for formula representation. SMILES is generally considered to have the advantage of being slightly more human-readable than InChI, the term SMILES refers to a line notation for encoding molecular structures and specific instances should strictly be called SMILES strings. However, the term SMILES is also used to refer to both a single SMILES string and a number of SMILES strings, the exact meaning is usually apparent from the context. The terms canonical and isomeric can lead to confusion when applied to SMILES. The terms describe different attributes of SMILES strings and are not mutually exclusive, typically, a number of equally valid SMILES strings can be written for a molecule. For example, CCO, OCC and CC all specify the structure of ethanol, algorithms have been developed to generate the same SMILES string for a given molecule, of the many possible strings, these algorithms choose only one of them. This SMILES is unique for each structure, although dependent on the algorithm used to generate it. These algorithms first convert the SMILES to a representation of the molecular structure. A common application of canonical SMILES is indexing and ensuring uniqueness of molecules in a database, there is currently no systematic comparison across commercial software to test if such flaws exist in those packages. SMILES notation allows the specification of configuration at tetrahedral centers, and these are structural features that cannot be specified by connectivity alone and SMILES which encode this information are termed isomeric SMILES
7.
Chemical formula
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These are limited to a single typographic line of symbols, which may include subscripts and superscripts. A chemical formula is not a name, and it contains no words. Although a chemical formula may imply certain simple chemical structures, it is not the same as a full chemical structural formula. Chemical formulas can fully specify the structure of only the simplest of molecules and chemical substances, the simplest types of chemical formulas are called empirical formulas, which use letters and numbers indicating the numerical proportions of atoms of each type. Molecular formulas indicate the numbers of each type of atom in a molecule. For example, the formula for glucose is CH2O, while its molecular formula is C6H12O6. This is possible if the relevant bonding is easy to show in one dimension, an example is the condensed molecular/chemical formula for ethanol, which is CH3-CH2-OH or CH3CH2OH. For reasons of structural complexity, there is no condensed chemical formula that specifies glucose, chemical formulas may be used in chemical equations to describe chemical reactions and other chemical transformations, such as the dissolving of ionic compounds into solution. A chemical formula identifies each constituent element by its chemical symbol, in empirical formulas, these proportions begin with a key element and then assign numbers of atoms of the other elements in the compound, as ratios to the key element. For molecular compounds, these numbers can all be expressed as whole numbers. For example, the formula of ethanol may be written C2H6O because the molecules of ethanol all contain two carbon atoms, six hydrogen atoms, and one oxygen atom. Some types of compounds, however, cannot be written with entirely whole-number empirical formulas. An example is boron carbide, whose formula of CBn is a variable non-whole number ratio with n ranging from over 4 to more than 6.5. When the chemical compound of the consists of simple molecules. These types of formulas are known as molecular formulas and condensed formulas. A molecular formula enumerates the number of atoms to reflect those in the molecule, so that the formula for glucose is C6H12O6 rather than the glucose empirical formula. However, except for very simple substances, molecular chemical formulas lack needed structural information, for simple molecules, a condensed formula is a type of chemical formula that may fully imply a correct structural formula. For example, ethanol may be represented by the chemical formula CH3CH2OH
8.
Density
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The density, or more precisely, the volumetric mass density, of a substance is its mass per unit volume. The symbol most often used for density is ρ, although the Latin letter D can also be used. Mathematically, density is defined as mass divided by volume, ρ = m V, where ρ is the density, m is the mass, and V is the volume. In some cases, density is defined as its weight per unit volume. For a pure substance the density has the numerical value as its mass concentration. Different materials usually have different densities, and density may be relevant to buoyancy, purity, osmium and iridium are the densest known elements at standard conditions for temperature and pressure but certain chemical compounds may be denser. Thus a relative density less than one means that the floats in water. The density of a material varies with temperature and pressure and this variation is typically small for solids and liquids but much greater for gases. Increasing the pressure on an object decreases the volume of the object, increasing the temperature of a substance decreases its density by increasing its volume. In most materials, heating the bottom of a results in convection of the heat from the bottom to the top. This causes it to rise relative to more dense unheated material, the reciprocal of the density of a substance is occasionally called its specific volume, a term sometimes used in thermodynamics. Density is a property in that increasing the amount of a substance does not increase its density. Archimedes knew that the irregularly shaped wreath could be crushed into a cube whose volume could be calculated easily and compared with the mass, upon this discovery, he leapt from his bath and ran naked through the streets shouting, Eureka. As a result, the term eureka entered common parlance and is used today to indicate a moment of enlightenment, the story first appeared in written form in Vitruvius books of architecture, two centuries after it supposedly took place. Some scholars have doubted the accuracy of this tale, saying among other things that the method would have required precise measurements that would have been difficult to make at the time, from the equation for density, mass density has units of mass divided by volume. As there are units of mass and volume covering many different magnitudes there are a large number of units for mass density in use. The SI unit of kilogram per metre and the cgs unit of gram per cubic centimetre are probably the most commonly used units for density.1,000 kg/m3 equals 1 g/cm3. In industry, other larger or smaller units of mass and or volume are often more practical, see below for a list of some of the most common units of density
9.
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
10.
Boiling point
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The boiling point of a substance is the temperature at which the vapor pressure of the liquid equals the pressure surrounding the liquid and the liquid changes into a vapor. The boiling point of a liquid varies depending upon the environmental pressure. A liquid in a vacuum has a lower boiling point than when that liquid is at atmospheric pressure. A liquid at high pressure has a boiling point than when that liquid is at atmospheric pressure. For a given pressure, different liquids boil at different temperatures, for example, water boils at 100 °C at sea level, but at 93.4 °C at 2,000 metres altitude. The normal boiling point of a liquid is the case in which the vapor pressure of the liquid equals the defined atmospheric pressure at sea level,1 atmosphere. At that temperature, the pressure of the liquid becomes sufficient to overcome atmospheric pressure. The standard boiling point has been defined by IUPAC since 1982 as the temperature at which boiling occurs under a pressure of 1 bar, the heat of vaporization is the energy required to transform a given quantity of a substance from a liquid into a gas at a given pressure. Liquids may change to a vapor at temperatures below their boiling points through the process of evaporation, evaporation is a surface phenomenon in which molecules located near the liquids edge, not contained by enough liquid pressure on that side, escape into the surroundings as vapor. On the other hand, boiling is a process in which molecules anywhere in the liquid escape, a saturated liquid contains as much thermal energy as it can without boiling. The saturation temperature is the temperature for a corresponding saturation pressure at which a liquid boils into its vapor phase, the liquid can be said to be saturated with thermal energy. Any addition of energy results in a phase transition. If the pressure in a system remains constant, a vapor at saturation temperature will begin to condense into its liquid phase as thermal energy is removed, similarly, a liquid at saturation temperature and pressure will boil into its vapor phase as additional thermal energy is applied. The boiling point corresponds to the temperature at which the pressure of the liquid equals the surrounding environmental pressure. Thus, the point is dependent on the pressure. Boiling points may be published with respect to the NIST, USA standard pressure of 101.325 kPa, at higher elevations, where the atmospheric pressure is much lower, the boiling point is also lower. The boiling point increases with increased pressure up to the critical point, the boiling point cannot be increased beyond the critical point. Likewise, the point decreases with decreasing pressure until the triple point is reached
11.
Safety data sheet
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A safety data sheet, material safety data sheet, or product safety data sheet is an important component of product stewardship, occupational safety and health, and spill-handling procedures. SDS formats can vary from source to source within a country depending on national requirements, SDSs are a widely used system for cataloging information on chemicals, chemical compounds, and chemical mixtures. SDS information may include instructions for the use and potential hazards associated with a particular material or product. The SDS should be available for reference in the area where the chemicals are being stored or in use, there is also a duty to properly label substances on the basis of physico-chemical, health and/or environmental risk. Labels can include hazard symbols such as the European Union standard symbols, a SDS for a substance is not primarily intended for use by the general consumer, focusing instead on the hazards of working with the material in an occupational setting. It is important to use an SDS specific to country and supplier, as the same product can have different formulations in different countries. The formulation and hazard of a product using a name may vary between manufacturers in the same country. Safety data sheets have made an integral part of the system of Regulation No 1907/2006. The SDS must be supplied in a language of the Member State where the substance or mixture is placed on the market. The 16 sections are, SECTION1, Identification of the substance/mixture, relevant identified uses of the substance or mixture and uses advised against 1.3. Details of the supplier of the safety data sheet 1.4, Emergency telephone number SECTION2, Hazards identification 2.1. Classification of the substance or mixture 2.2, Other hazards SECTION3, Composition/information on ingredients 3.1. Mixtures SECTION4, First aid measures 4.1, Description of first aid measures 4.2. Most important symptoms and effects, both acute and delayed 4.3, indication of any immediate medical attention and special treatment needed SECTION5, Firefighting measures 5.1. Special hazards arising from the substance or mixture 5.3, advice for firefighters SECTION6, Accidental release measure 6.1. Personal precautions, protective equipment and emergency procedures 6.2, methods and material for containment and cleaning up 6.4. Reference to other sections SECTION7, Handling and storage 7.1, conditions for safe storage, including any incompatibilities 7.3. Specific end use SECTION8, Exposure controls/personal protection 8.1, Exposure controls SECTION9, Physical and chemical properties 9.1
12.
Flash point
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The flash point is the lowest temperature at which vapours of a volatile material will ignite, when given an ignition source. The flash point may sometimes be confused with the autoignition temperature, the fire point is the lowest temperature at which the vapor will keep burning after being ignited and the ignition source removed. The fire point is higher than the point, because at the flash point the vapor may be reliably expected to cease burning when the ignition source is removed. The flash point is a characteristic that is used to distinguish between flammable liquids, such as petrol, and combustible liquids, such as diesel. It is also used to characterize the fire hazards of liquids, all liquids have a specific vapor pressure, which is a function of that liquids temperature and is subject to Boyles Law. As temperature increases, vapor pressure increases, as vapor pressure increases, the concentration of vapor of a flammable or combustible liquid in the air increases. Hence, temperature determines the concentration of vapor of the liquid in the air. The flash point is the lowest temperature at which there will be enough flammable vapor to induce ignition when a source is applied. There are two types of flash point measurement, open cup and closed cup. In open cup devices, the sample is contained in a cup which is heated and, at intervals. The measured flash point will vary with the height of the flame above the liquid surface and, at sufficient height. The best-known example is the Cleveland open cup, in both these types, the cups are sealed with a lid through which the ignition source can be introduced. Closed cup testers normally give lower values for the point than open cup and are a better approximation to the temperature at which the vapour pressure reaches the lower flammable limit. The flash point is an empirical measurement rather than a physical parameter. The measured value will vary with equipment and test protocol variations, including temperature ramp rate, time allowed for the sample to equilibrate, sample volume, methods for determining the flash point of a liquid are specified in many standards. For example, testing by the Pensky-Martens closed cup method is detailed in ASTM D93, IP34, ISO2719, DIN51758, JIS K2265 and AFNOR M07-019. Determination of flash point by the Small Scale closed cup method is detailed in ASTM D3828 and D3278, EN ISO3679 and 3680, cEN/TR15138 Guide to Flash Point Testing and ISO TR29662 Guidance for Flash Point Testing cover the key aspects of flash point testing. Gasoline is a used in a spark-ignition engine
13.
Ketone
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In chemistry, a ketone /ˈkiːtoʊn/ is an organic compound with the structure RCR, where R and R can be a variety of carbon-containing substituents. Ketones and aldehydes are simple compounds that contain a carbonyl group and they are considered simple because they do not have reactive groups like −OH or −Cl attached directly to the carbon atom in the carbonyl group, as in carboxylic acids containing −COOH. Many ketones are known and many are of importance in industry. Examples include many sugars and the industrial solvent acetone, which is the smallest ketone, the word ketone is derived from Aketon, an old German word for acetone. According to the rules of IUPAC nomenclature, ketones are named by changing the suffix -ane of the parent alkane to -anone, the position of the carbonyl group is usually denoted by a number. For the most important ketones, however, traditional names are still generally used. The common names of ketones are obtained by writing separately the names of the two alkyl groups attached to the group, followed by ketone as a separate word. The names of the groups are written alphabetically. When the two groups are the same, the prefix di- is added before the name of alkyl group. The positions of other groups are indicated by Greek letters, the α-carbon being the adjacent to carbonyl group. If both alkyl groups in a ketone are the same then the ketone is said to be symmetrical, although used infrequently, oxo is the IUPAC nomenclature for a ketone functional group. Other prefixes, however, are also used, for some common chemicals, keto or oxo refer to the ketone functional group. The term oxo is used widely through chemistry, for example, it also refers to an oxygen atom bonded to a transition metal. The ketone carbon is often described as sp2 hybridized, a description that includes both their electronic and molecular structure, ketones are trigonal planar around the ketonic carbon, with C−C−O and C−C−C bond angles of approximately 120°. Ketones differ from aldehydes in that the group is bonded to two carbons within a carbon skeleton. In aldehydes, the carbonyl is bonded to one carbon and one hydrogen and are located at the ends of carbon chains, ketones are also distinct from other carbonyl-containing functional groups, such as carboxylic acids, esters and amides. The carbonyl group is polar because the electronegativity of the oxygen is greater than that for carbon, thus, ketones are nucleophilic at oxygen and electrophilic at carbon. Because the carbonyl group interacts with water by bonding, ketones are typically more soluble in water than the related methylene compounds
14.
Organic chemistry
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Study of structure includes many physical and chemical methods to determine the chemical composition and the chemical constitution of organic compounds and materials. In the modern era, the range extends further into the table, with main group elements, including, Group 1 and 2 organometallic compounds. They either form the basis of, or are important constituents of, many products including pharmaceuticals, petrochemicals and products made from them, plastics, fuels and explosives. Before the nineteenth century, chemists generally believed that compounds obtained from living organisms were endowed with a force that distinguished them from inorganic compounds. According to the concept of vitalism, organic matter was endowed with a vital force, during the first half of the nineteenth century, some of the first systematic studies of organic compounds were reported. Around 1816 Michel Chevreul started a study of soaps made from various fats and he separated the different acids that, in combination with the alkali, produced the soap. Since these were all compounds, he demonstrated that it was possible to make a chemical change in various fats, producing new compounds. In 1828 Friedrich Wöhler produced the chemical urea, a constituent of urine, from inorganic starting materials. The event is now accepted as indeed disproving the doctrine of vitalism. In 1856 William Henry Perkin, while trying to manufacture quinine accidentally produced the organic dye now known as Perkins mauve and his discovery, made widely known through its financial success, greatly increased interest in organic chemistry. A crucial breakthrough for organic chemistry was the concept of chemical structure, ehrlich popularized the concepts of magic bullet drugs and of systematically improving drug therapies. His laboratory made decisive contributions to developing antiserum for diphtheria and standardizing therapeutic serums, early examples of organic reactions and applications were often found because of a combination of luck and preparation for unexpected observations. The latter half of the 19th century however witnessed systematic studies of organic compounds, the development of synthetic indigo is illustrative. The production of indigo from plant sources dropped from 19,000 tons in 1897 to 1,000 tons by 1914 thanks to the methods developed by Adolf von Baeyer. In 2002,17,000 tons of indigo were produced from petrochemicals. In the early part of the 20th Century, polymers and enzymes were shown to be large organic molecules, the multiple-step synthesis of complex organic compounds is called total synthesis. Total synthesis of natural compounds increased in complexity to glucose. For example, cholesterol-related compounds have opened ways to synthesize complex human hormones, since the start of the 20th century, complexity of total syntheses has been increased to include molecules of high complexity such as lysergic acid and vitamin B12
15.
Soman
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Soman, or GD, is an extremely toxic chemical substance. It is an agent, interfering with normal functioning of the mammalian nervous system by inhibiting the enzyme cholinesterase. It is an inhibitor of both acetylcholinesterase and butyrylcholinesterase, as a chemical weapon, it is classified as a weapon of mass destruction by the United Nations according to UN Resolution 687. Its production is controlled, and stockpiling is outlawed by the Chemical Weapons Convention of 1993 where it is classified as a Schedule 1 substance. Soman was the third of the so-called G-series nerve agents to be discovered along with GA, GB and it is a volatile, corrosive, and colorless liquid with a faint odor when pure. More commonly, it is a yellow to brown color and has an odor described as similar to camphor. The LCt50 for soman is 70 mg·min/m3 in humans and it is both more lethal and more persistent than sarin or tabun, but less so than cyclosarin. GD can be thickened for use as a chemical spray using an acryloid copolymer and it can also be deployed as a binary chemical weapon, its precursor chemicals are methylphosphonyl difluoride and a mixture of pinacolyl alcohol and an amine. After World War I, during which mustard gas and phosgene were used as warfare agents. Nevertheless, research into chemical warfare agents and the use of them continued, in 1936 a new, more dangerous chemical agent was discovered when Gerhard Schrader of IG Farben in Germany isolated tabun, the first nerve agent, while developing new insecticides. This discovery was followed by the isolation of sarin in 1938, during World War II, research into nerve agents continued in the United States and Germany. In summer 1944, soman, a liquid with a camphor odor, was developed by the Germans. Soman proved to be more toxic than tabun and sarin. Nobel Laureate Richard Kuhn together with Konrad Henkel discovered soman during research into the pharmacology of tabun and this research was commissioned by the German Army. Soman was produced in quantities at a pilot plant at the IG Farben factory in Ludwigshafen. It was never used in World War II, just as tabun, producing or stockpiling soman was banned by the 1993 Chemical Weapons Convention. When the convention entered force, the parties declared world-wide stockpiles of 9,057 tonnes of soman, as of December 2015, 84% of the stockpiles had been destroyed. The crystal structure of soman complexed with acetylcholinesterase was determined by Millard et al. by X-ray crystallography, Soman has a phosphonyl group with a fluoride and a hydrocarbon covalently bound to it
16.
Australia Group
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The group, initially consisting of 15 members, held its first meeting in Brussels, Belgium, in September 1989. With the incorporation of Mexico on August 12,2013, it now has 42 members, including the European Commission, all 28 member states of the European Union, Ukraine, the name comes from Australias initiative to create the group. The initial members of the group had different assessments of which chemical precursors should be subject to export control, later adherents initially had no such controls. In 2002, the group took two important steps to export control. Delegations representing the members every year in Paris, France. Arms control List of Schedule 3 substances The Australia Group homepage
17.
Pinacol rearrangement
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The pinacol–pinacolone rearrangement is a method for converting a 1, 2-diol to a carbonyl compound in organic chemistry. The 1, 2-rearrangement takes place under acidic conditions, the name of the rearrangement reaction comes from the rearrangement of pinacol to pinacolone. This reaction was first described by Wilhelm Rudolph Fittig in 1860 of the famed Fittig reaction involving coupling of 2 aryl halides in presence of metal in dry ethereal solution. In the course of this reaction, protonation of one of the –OH groups occurs. If both the –OH groups are not alike, then the one which yields a stable carbocation participates in the reaction. Subsequently, a group from the adjacent carbon migrates to the carbocation center. The driving force for this rearrangement step is believed to be the stability of the resultant oxonium ion. The migration of alkyl groups in this reaction occurs in accordance with their usual migratory aptitude, the conclusion which group stabilizes carbocation more effectively is migrated In cyclic systems, the reaction presents more features of interest. In these reactions, the stereochemistry of the plays a crucial role in deciding the major product. An alkyl group which is situated trans- to the leaving –OH group alone may migrate, if otherwise, ring expansion occurs, i. e. the ring carbon itself migrates to the carbocation centre. This reveals another interesting feature of the reaction, viz. that it is largely concerted, there appears to be a connection between the migration origin and migration terminus throughout the reaction. Moreover, if the alkyl group has a chiral center as its key atom. Although Fittig first published about the pinacol rearrangement, it was not Fittig, in an 1859 publication Wilhelm Rudolph Fittig described the reaction of acetone with potassium metal. Fittig wrongly assumed a molecular formula of n for acetone, the result of an atomic weight debate finally settled at the Karlsruhe Congress in 1860. He also wrongly believed acetone to be an alcohol which he hoped to prove by forming an alkoxide salt. The reaction product he obtained instead he called paraceton which he believed to be an acetone dimer, in his second publication in 1860 he reacted paraceton with sulfuric acid. Again Fittig was unable to assign a structure to the reaction product which he assumed to be another isomer or a polymer. Contemporary chemists who had adapted to the new atomic weight reality did not fare better
18.
1,4-Dioxane
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1, 4-Dioxane is a heterocyclic organic compound, classified as an ether. It is a liquid with a faint sweet odor similar to that of diethyl ether. The compound is called simply dioxane because the other dioxane isomers are rarely encountered. Dioxane is used as a solvent for a variety of applications as well as in the laboratory. Dioxane is produced by the dehydration of diethylene glycol, which in turn is obtained from the hydrolysis of ethylene oxide. In 1985, the production capacity for dioxane was between 11,000 and 14,000 tons. In 1990, the total U. S. production volume of dioxane was between 5,250 and 9,150 tons, the dioxane molecule is centrosymmetric, meaning that it adopts a chair conformation, typical of relatives of cyclohexane. However, the molecule is conformationally flexible, and the conformation is easily adopted. In the 1980s, most of the produced was used as a stabilizer for 1,1, 1-trichloroethane for storage. Dioxane poisons this catalysis reaction by forming an adduct with aluminum trichloride, Dioxane is used in a variety of applications as a versatile aprotic solvent, e. g. for inks, adhesives, and cellulose esters. It is substituted for tetrahydrofuran in some processes, because of its lower toxicity, while diethyl ether is rather insoluble in water, dioxane is miscible and in fact is hygroscopic. At standard pressure, the mixture of water and dioxane in the ratio 17.9,82.1 by mass is an azeotrope that boils at 87.6 C. The oxygen atoms are Lewis basic, and so dioxane is able to solvate many inorganic compounds and it reacts with Grignard reagents to precipitate the magnesium dihalide. In this way, dioxane is used to drive the Schlenk equilibrium, dimethylmagnesium is prepared in this manner,2 CH3MgBr +2 → MgBr22 + 2Mg Dioxane is used as an internal standard for proton NMR spectroscopy in D2O. Dioxane has an LD50 of 5170 mg/kg in rats and this compound is irritating to the eyes and respiratory tract. Exposure may cause damage to the nervous system, liver. In a 1978 mortality study conducted on workers exposed to 1, 4-Dioxane, Dioxane is classified by the National Toxicology Program as reasonably anticipated to be a human carcinogen. It is also classified by the IARC as a Group 2B carcinogen, the U. S. Environmental Protection Agency classifies dioxane as a probable human carcinogen, and a known irritant at concentrations significantly higher than those found in commercial products
19.
Prins reaction
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The Prins reaction is an organic reaction consisting of an electrophilic addition of an aldehyde or ketone to an alkene or alkyne followed by capture of a nucleophile. The outcome of the reaction depends on reaction conditions, with water and a protic acid such as sulfuric acid as the reaction medium and formaldehyde the reaction product is a 1, 3-diol. When water is absent, the intermediate loses a proton to give an allylic alcohol. With an excess of formaldehyde and a low temperature the reaction product is a dioxane. When water is replaced by acetic acid the corresponding esters are formed, the original reactants employed by Dutch chemist Hendrik Jacobus Prins in his 1919 publication were styrene, pinene, camphene, eugenol, isosafrole and anethole. In 1937 the reaction was investigated as part of a quest for di-olefins to be used in synthetic rubber, the reaction mechanism for this reaction is depicted in scheme 5. The carbonyl reactant is protonated by an acid and for the resulting oxonium ion 3 two resonance structures can be drawn. This electrophile engages in an addition with the alkene to the carbocationic intermediate 4. Exactly how much charge is present on the secondary carbon atom in this intermediate should be determined for each reaction set. Evidence exists for neighbouring group participation of the oxygen or its neighboring carbon atom. When the overall reaction has a degree of concertedness, the charge built-up will be modest. In this mode the positive charge is dispersed over oxygen and carbon in the resonance structures 8a, ring closure leads through intermediate 9 to the dioxane 10. An example is the conversion of styrene to 4-phenyl-m-dioxane. in gray, only in specific reactions, the photochemical Paternò–Büchi reaction between alkenes and aldehydes to oxetanes is more straightforward. Many variations of the Prins reaction exist because it lends itself easily to cyclization reactions, the halo-Prins reaction is one such modification with replacement of protic acids and water by lewis acids such as stannic chloride and boron tribromide. The halogen is now the nucleophile recombining with the carbocation and this observed cis diastereoselectivity is due to the intermediate formation of a trichlorotitanium alkoxide making possible an easy delivery of chlorine to the carbocation ion from the same face. The trans isomer is preferred when the switch is made to a tin tetrachloride reaction at room temperature, the Prins-pinacol reaction is a cascade reaction of a Prins reaction and a pinacol rearrangement. The carbonyl group in the reactant in scheme 8 is masked as a dimethyl acetal and the hydroxyl group is masked as a triisopropylsilyl ether. org
20.
Ketonic decarboxylation
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The reaction mechanism likely involves nucleophilic attack of the alpha-carbon of one acid group on the other acid groups carbonyl, possibly as a concerted reaction with the decarboxylation. With two different carboxylic acids, the reaction behaves poorly because of poor selectivity except when one of the acids is used in large excess. The dry distillation of calcium acetate to acetone was reported by Charles Friedel in 1858, ketonic decarboxylation of propanoic acid over a manganese oxide catalyst in a tube furnace affords the synthesis of 3-pentanone. Of commercial importance is the production of 3-pentanone from propionic acid with cerium oxide. An example of intramolecular ketonization is the conversion of acid to cyclopentanone with barium hydroxide
21.
Pivalic acid
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Pivalic acid is a carboxylic acid with a molecular formula of 3CCO2H. This colourless, odiferous organic compound is solid at room temperature, the acronym for pivalate is Piv & for pivalic acid it is PivH. Pivalic acid is prepared by hydrocarboxylation of isobutene via the Koch reaction, tert-Butyl alcohol and isobutyl alcohol can also be used in place of isobutene. Globally, several million kilograms are produced annually, pivalic acid is also economically recovered as a by-product from the production of semi-synthetic penicillins like ampicillin and amoxycillin. It was originally prepared by the oxidation of pinacolone with chromic acid, convenient laboratory routes proceed via t-butyl chloride via carbonation of the Grignard reagent and by oxidation of pinacolone. Relative to esters of most carboxylic acids, esters of pivalic acid are unusually resistant to hydrolysis, some applications result from this thermal stability. Polymers derived from pivalate esters of vinyl alcohol are highly reflective lacquers, the pivaloyl group is a protective group for alcohols in organic synthesis. Pivalic acid is used as an internal chemical shift standard for NMR spectra of aqueous solutions. While DSS is more used for this purpose, the minor peaks from protons on the three methylene bridges in DSS can be problematic. The 1H NMR spectrum at 25 °C and neutral pH is a singlet at 1.08 ppm, pivaloyl group is used as a protecting group in organic synthesis. See for example, it is employed in the preparation of Sivelestat, Common protection methods include treatment of alcohol with pivaloyl chloride in presence of pyridine. Alternatively, the esters can be prepared using pivaloic anhydride in the presence of Sc3 or VO2 Common deprotection methods involve hydrolysis with the base or other nucleophiles
22.
Retrosynthetic analysis
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Retrosynthetic analysis is a technique for solving problems in the planning of organic syntheses. This is achieved by transforming a target molecule into simpler precursor structures without assumptions regarding starting materials, each precursor material is examined using the same method. This procedure is repeated until simple or commercially available structures are reached, corey formalized this concept in his book The Logic of Chemical Synthesis. The power of retrosynthetic analysis becomes evident in the design of a synthesis, the goal of retrosynthetic analysis is structural simplification. Often, a synthesis will have more than one possible synthetic route, retrosynthesis is well suited for discovering different synthetic routes and comparing them in a logical and straightfoward fashion. A database may be consulted at each stage of the analysis, in that case, no further exploration of that compound would be required. Disconnection A retrosynthetic step involving the breaking of a bond to form two synthons, retron A minimal molecular substructure that enables certain transformations. Retrosynthetic tree A directed acyclic graph of several possible retrosyntheses of a single target, a synthon and the corresponding commercially available synthetic equivalent are shown below, Target The desired final compound. Transform The reverse of a reaction, the formation of starting materials from a single product. An example will allow the concept of analysis to be easily understood. In planning the synthesis of phenylacetic acid, two synthons are identified, a nucleophilic -COOH group, and an electrophilic PhCH2+ group. Of course, both synthons do not exist per se, synthetic equivalents corresponding to the synthons are reacted to produce the desired product. In this case, the anion is the synthetic equivalent for the −COOH synthon. Manipulation of functional groups can lead to significant reductions in molecular complexity, numerous chemical targets have distinct stereochemical demands. Stereochemical transformations can remove or transfer the desired chirality thus simplifying the target, directing a synthesis toward a desirable intermediate can greatly narrow the focus of an analysis. The application of transformations to retrosynthetic analysis can lead to reductions in molecular complexity. Unfortunately, powerful transform-based retrons are rarely present in complex molecules, disconnections that preserve ring structures are encouraged. Disconnections that create rings larger than 7 members are discouraged, retrosynthesis planning tool, ICSynth by InfoChem
23.
Stiripentol
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Stiripentol is an anticonvulsant drug used in the treatment of epilepsy. It is approved for the treatment of Dravet syndrome, an epilepsy syndrome and it is unrelated to other anticonvulsants and belongs to the group of aromatic allylic alcohols. As with most anticonvulsants, the mechanism of action is unknown. Regardless, stiripentol has been shown to have anticonvulsant effects of its own and it has also been shown to increase GABA levels in brain tissues by interfering with its reuptake and metabolism. Specifically, it has shown to inhibit lactate dehydrogenase, which is an important enzyme involved in the energy metabolism of neurons. Inhibition of this enzyme can make neurons less prone to fire action potentials, Stiripentol also improves the effectiveness of many other anticonvulsants, possibly due to its inhibition of certain enzymes, slowing the drugs metabolism and increasing blood plasma levels. In December 2001 the European Medicines Agency granted stiripentol orphan drug status for the treatment of severe myoclonic epilepsy of infancy, on 4 January 2007, the EMA granted the drug a marketing authorisation that is valid throughout the European Union. It is indicated as a therapy with sodium valproate and clobazam for treating Dravet syndrome whose seizures are not adequately controlled with clobazam. Children with SMEI develop often intractable seizures during their first year of life, small-scale trials have shown remarkably high response rates, with a significant minority of those treated becoming seizure free. In addition, it may be used to treat refractory childhood epilepsy in conjunction with carbamazepine and it appears to be less effective in adolescents and adults. Stiripentol is available as a capsule and as a sachet of powder to make a drinkable suspension. Initial dose is 50 mg/kg per day and this may be increased up to 100 mg/kg per day, with a maximum of 4 g/day. The dose is to be divided into two or three and to be taken with meals, the dose of other anticonvulsants may have to be reduced. Side effects are due to the increase in plasma concentrations of other anticonvulsants. Nausea and vomiting are particularly noted when used in combination with sodium valproate, Stiripentol inhibits several cytochrome P450 isoenzymes and so interacts with many anticonvulsants and other medicines. This is both a strength and weakness and it appears to increase the potency of phenobarbital, primidone, phenytoin, carbamazepine, clobazam and diazepam. For example, blood levels of carbamazepine can be maintained while reducing the dose by 50%, Tran A, Vauzelle-Kervroedan F, Rey E, et al. Effect of stiripentol on carbamazepine plasma concentration and metabolism in epileptic children, perez J, Chiron C, Musial C, et al
24.
Paclobutrazol
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Paclobutrazol is a plant growth retardant and triazole fungicide. It is a known antagonist of the plant hormone gibberellin, PBZ has also been shown to reduce frost sensitivity in plants. PBZ is used by arborists to reduce growth and has been shown to have additional positive effects on trees. Among those are improved resistance to stress, darker green leaves, higher resistance against fungi and bacteria. Cambial growth, as well as growth, has been shown to be reduced in some tree species. PBZ is normally applied to the soil to be taken up by the roots, seeds can be soaked with PBZ to reduce seedling growth. Paclobutrazol in the Pesticide Properties DataBase
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