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.
Solubility
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Solubility is the property of a solid, liquid, or gaseous chemical substance called solute to dissolve in a solid, liquid, or gaseous solvent. The solubility of a substance depends on the physical and chemical properties of the solute and solvent as well as on temperature, pressure. The solubility of a substance is a different property from the rate of solution. Most often, the solvent is a liquid, which can be a substance or a mixture. One may also speak of solid solution, but rarely of solution in a gas, the extent of solubility ranges widely, from infinitely soluble such as ethanol in water, to poorly soluble, such as silver chloride in water. The term insoluble is often applied to poorly or very poorly soluble compounds, a common threshold to describe something as insoluble is less than 0.1 g per 100 mL of solvent. Under certain conditions, the solubility can be exceeded to give a so-called supersaturated solution. Metastability of crystals can also lead to apparent differences in the amount of a chemical that dissolves depending on its form or particle size. A supersaturated solution generally crystallises when seed crystals are introduced and rapid equilibration occurs, phenylsalicylate is one such simple observable substance when fully melted and then cooled below its fusion point. Solubility is not to be confused with the ability to dissolve a substance, for example, zinc dissolves in hydrochloric acid as a result of a chemical reaction releasing hydrogen gas in a displacement reaction. The zinc ions are soluble in the acid, the smaller a particle is, the faster it dissolves although there are many factors to add to this generalization. Crucially solubility applies to all areas of chemistry, geochemistry, inorganic, physical, organic, in all cases it will depend on the physical conditions and the enthalpy and entropy directly relating to the solvents and solutes concerned. By far the most common solvent in chemistry is water which is a solvent for most ionic compounds as well as a range of organic substances. This is a factor in acidity/alkalinity and much environmental and geochemical work. According to the IUPAC definition, solubility is the composition of a saturated solution expressed as a proportion of a designated solute in a designated solvent. Solubility may be stated in units of concentration such as molarity, molality, mole fraction, mole ratio, mass per volume. Solubility occurs under dynamic equilibrium, which means that solubility results from the simultaneous and opposing processes of dissolution, the solubility equilibrium occurs when the two processes proceed at a constant rate. The term solubility is used in some fields where the solute is altered by solvolysis
12.
Ethanol
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Ethanol, also called alcohol, ethyl alcohol, and drinking alcohol, is the principal type of alcohol found in alcoholic beverages. It is a volatile, flammable, colorless liquid with a characteristic odor. Its chemical formula is C 2H 6O, which can be written also as CH 3-CH 2-OH or C 2H 5-OH, ethanol is mostly produced by the fermentation of sugars by yeasts, or by petrochemical processes. It is a psychoactive drug, causing a characteristic intoxication. It is widely used as a solvent, as fuel, and as a feedstock for synthesis of other chemicals, the eth- prefix and the qualifier ethyl in ethyl alcohol originally come from the name ethyl assigned in 1834 to the group C 2H 5- by Justus Liebig. He coined the word from the German name Aether of the compound C 2H 5-O-C 2H5, according to the Oxford English Dictionary, Ethyl is a contraction of the Ancient Greek αἰθήρ and the Greek word ύλη. The name ethanol was coined as a result of a resolution that was adopted at the International Conference on Chemical Nomenclature that was held in April 1892 in Geneva, Switzerland. The term alcohol now refers to a class of substances in chemistry nomenclature. The Oxford English Dictionary claims that it is a loan from Arabic al-kuḥl, a powdered ore of antimony used since aniquity as a cosmetic. The use of alcohol for ethanol is modern, first recorded 1753, the systematic use in chemistry dates to 1850. Ethanol is used in medical wipes and most common antibacterial hand sanitizer gels as an antiseptic, ethanol kills organisms by denaturing their proteins and dissolving their lipids and is effective against most bacteria and fungi, and many viruses. However, ethanol is ineffective against bacterial spores, ethanol may be administered as an antidote to methanol and ethylene glycol poisoning. Ethanol, often in high concentrations, is used to dissolve many water-insoluble medications, as a central nervous system depressant, ethanol is one of the most commonly consumed psychoactive drugs. The amount of ethanol in the body is typically quantified by blood alcohol content, small doses of ethanol, in general, produce euphoria and relaxation, people experiencing these symptoms tend to become talkative and less inhibited, and may exhibit poor judgment. Ethanol is commonly consumed as a drug, especially while socializing. The largest single use of ethanol is as a fuel and fuel additive. Brazil in particular relies heavily upon the use of ethanol as an engine fuel, gasoline sold in Brazil contains at least 25% anhydrous ethanol. Hydrous ethanol can be used as fuel in more than 90% of new gasoline fueled cars sold in the country, Brazilian ethanol is produced from sugar cane and noted for high carbon sequestration
13.
Hydrochloric acid
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Hydrochloric acid is a corrosive, strong mineral acid with many industrial uses. A colorless, highly pungent solution of chloride in water. Free hydrochloric acid was first formally described in the 16th century by Libavius, later, it was used by chemists such as Glauber, Priestley, and Davy in their scientific research. It has numerous applications, including household cleaning, production of gelatin and other food additives, descaling. About 20 million tonnes of acid are produced worldwide annually. It is also found naturally in gastric acid, Hydrochloric acid was known to European alchemists as spirits of salt or acidum salis. Both names are used, especially in other languages, such as German, Salzsäure, Dutch, Zoutzuur, Swedish, Saltsyra, Turkish, Tuz Ruhu, Polish, kwas solny and Chinese. Gaseous HCl was called marine acid air, the old name muriatic acid has the same origin, and this name is still sometimes used. The name hydrochloric acid was coined by the French chemist Joseph Louis Gay-Lussac in 1814, aqua regia, a mixture consisting of hydrochloric and nitric acids, prepared by dissolving sal ammoniac in nitric acid, was described in the works of Pseudo-Geber, a 13th-century European alchemist. Other references suggest that the first mention of aqua regia is in Byzantine manuscripts dating to the end of the 13th century, free hydrochloric acid was first formally described in the 16th century by Libavius, who prepared it by heating salt in clay crucibles. Joseph Priestley of Leeds, England prepared pure hydrogen chloride in 1772, during the Industrial Revolution in Europe, demand for alkaline substances increased. A new industrial process developed by Nicolas Leblanc of Issoundun, France enabled cheap large-scale production of sodium carbonate, in this Leblanc process, common salt is converted to soda ash, using sulfuric acid, limestone, and coal, releasing hydrogen chloride as a by-product. Until the British Alkali Act 1863 and similar legislation in other countries, after the passage of the act, soda ash producers were obliged to absorb the waste gas in water, producing hydrochloric acid on an industrial scale. In the 20th century, the Leblanc process was replaced by the Solvay process without a hydrochloric acid by-product. Since hydrochloric acid was already settled as an important chemical in numerous applications. After the year 2000, hydrochloric acid is made by absorbing by-product hydrogen chloride from industrial organic compounds production. Hydrochloric acid is the salt of hydronium ion, H3O+ and chloride and it is usually prepared by treating HCl with water. H C l + H2 O ⟶ H3 O + + C l − Hydrochloric acid can therefore be used to prepare salts called chlorides, Hydrochloric acid is a strong acid, since it is completely dissociated in water
14.
Distilled water
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Distilled water is water that has had many of its impurities removed through distillation. Distillation involves boiling the water and then condensing the steam into a clean container, drinking water has been distilled from sea water since at least about AD200, when the process was clearly described by Alexander of Aphrodisias. Its history predates this, as a passage in Aristotles Meteorologica refers to the distillation of water, captain Israel Williams of the Friendship improvised a way to distill water, which he described in his journal. In chemical and biological laboratories, as well as in industry, but if these alternatives are not pure enough, distilled water is used. If exceptionally high purity water is required, double distilled water is used, distilled water is also commonly used to top off lead acid batteries used in cars and trucks. The presence of other commonly found in tap water will drastically reduce an automobile batterys lifespan. Distilled water is preferable to tap water for use in cooling systems. Distilled water is preferable to tap water for use in model steam engine boilers. Mineral build-up resulting from the use of tap water in model boilers can severely reduce the efficiency of the boilers if run for long periods and this build-up is known as boiler scale. Some people use distilled water for aquariums because it lacks the chemicals found in tap water. It is important to supplement distilled water when using it for fishkeeping, distilled water is also essential for use in cigar humidors. Mineral build-up resulting from the use of tap water will reduce the effectiveness of the humidor, in contrast, some home brewers who want to brew a traditional European Pilsner will dilute their hard water with distilled water so as to mimic the soft waters of Pilsen. Another application was to increase the density of the air to assist early airplane jet engines during takeoff in hot and high atmospheric conditions, distilled water is also used in Constant Positive Airway Pressure machines to humidify the air entering the users nasal cavity, mouth, and throat. Distilled water will not leave any contaminants behind when the humidifier in the CPAP machine evaporates the water, although possibly once the recommended procedure, using distilled water in steam irons for pressing clothes, is no longer necessary. Now most manufacturers say that water is unnecessary in their irons. It has been suggested that this water in an iron will flash boil when disturbed, and cause the iron to spit, leak. Until World War II, distilling sea water to fresh water was time-consuming. The saying was, It takes one gallon of fuel to one gallon of fresh water
15.
Indole
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Indole is an aromatic heterocyclic organic compound with formula C8H7N. It has a structure, consisting of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring. Indole is widely distributed in the environment and can be produced by a variety of bacteria. As an intercellular signal molecule, indole regulates various aspects of physiology, including spore formation, plasmid stability, resistance to drugs, biofilm formation. The amino acid tryptophan is a derivative and the precursor of the neurotransmitter serotonin. Indole is a solid at room temperature, Indole can be produced by bacteria as a degradation product of the amino acid tryptophan. It occurs naturally in feces and has an intense fecal odor. At very low concentrations, however, it has a flowery smell and it also occurs in coal tar. The corresponding substituent is called indolyl, Indole undergoes electrophilic substitution, mainly at position 3. Substituted indoles are structural elements of the tryptophan-derived tryptamine alkaloids like the neurotransmitter serotonin, other indolic compounds include the plant hormone auxin, tryptophol, the anti-inflammatory drug indomethacin, the betablocker pindolol, and the naturally occurring hallucinogen dimethyltryptamine. The name indole is a portmanteau of the indigo and oleum. Indole chemistry began to develop with the study of the dye indigo, indigo can be converted to isatin and then to oxindole. Then, in 1866, Adolf von Baeyer reduced oxindole to indole using zinc dust, in 1869, he proposed a formula for indole. Certain indole derivatives were important dyestuffs until the end of the 19th century, in the 1930s, interest in indole intensified when it became known that the indole substituent is present in many important alkaloids, and it remains an active area of research today. It condenses with serine by Michael addition of indole to PLP-aminoacrylate, as an intercellular signal molecule, indole regulates various aspects of bacterial physiology, including spore formation, plasmid stability, resistance to drugs, biofilm formation, and virulence. The amino acid tryptophan is a derivative and the precursor of the neurotransmitter serotonin. Indole is a constituent of coal tar, and the 220–260 °C distillation fraction is the main industrial source of the material. Indole and its derivatives can also be synthesized by a variety of methods, the main industrial routes start from aniline via vapor-phase reaction with ethylene glycol in the presence of catalysts, In general, reactions are conducted between 200 and 500 °C
16.
Proanthocyanidin
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Proanthocyanidins are a class of polyphenols found in a variety of plants. Many are oligomers of catechin and epicatechin and their gallic acid esters, more complex polyphenols, having the same polymeric building block, form the group of tannins. Proanthocyanidins were discovered in 1947 by Jacques Masquelier, who developed and patented techniques for the extraction of oligomeric proanthocyanidins from pine bark, however, bilberry, cranberry, black currant, green tea, black tea, and other plants also contain these flavonoids. Cocoa beans contain the highest concentrations, proanthocyanidins also may be isolated from Quercus petraea and Q. robur heartwood. Açaí oil, obtained from the fruit of the palm, is rich in numerous procyanidin oligomers. Apples contain on average per serving about eight times the amount of found in wine, with some of the highest amounts found in the Red Delicious. An extract of maritime pine bark called Pycnogenol bears 65-75 percent proanthocyanidins, thus a 100 mg serving would contain 65 to 75 mg of proanthocyanidins. Proanthocyanidin glycosides can be isolated from cocoa liquor, the seed testas of field beans contain proanthocyanidins that affect the digestibility in piglets and could have an inhibitory activity on enzymes. Cistus salviifolius also contains oligomeric proanthocyanidins, condensed tannins may be characterised by a number of techniques including depolymerisation, asymmetric flow field flow fractionation or small-angle X-ray scattering. DMACA is a dye that is useful for localization of proanthocyanidin compounds in plant histology. The use of the reagent results in blue staining and it can also be used to titrate proanthocyanidins. Proanthocyanidins from field beans or barley have been estimated using the vanillin-HCl method, proanthocyanidins can be titrated using the Procyanidolic Index. It is a method that measures the change in color when the product is mixed with certain chemicals. The greater the changes, the higher the PCOs content is. However, the Procyanidolic Index is a value that can measure well over 100. Unfortunately, a Procyanidolic Index of 95 was erroneously taken to mean 95% PCO by some, all current methods of analysis suggest that the actual PCO content of these products is much lower than 95%. Gel permeation chromatography analysis allows separation of monomers from larger proanthocyanidin molecules, monomers of proanthocyanidins can be characterized by analysis with HPLC and mass spectrometry. Tandem mass spectrometry can be used to sequence proanthocyanidins, oligomeric proanthocyanidins strictly refer to dimer and trimer polymerizations of catechins
17.
Flavonoid
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Flavonoids are a class of plant and fungus secondary metabolites. Chemically, flavonoids have the structure of a 15-carbon skeleton. This carbon structure can be abbreviated C6-C3-C6 and this class was the first to be termed bioflavonoids. The terms flavonoid and bioflavonoid have also more loosely used to describe non-ketone polyhydroxy polyphenol compounds which are more specifically termed flavanoids. The three cycle or heterocycles in the backbone are generally called ring A, B and C. Ring A usually shows a phloroglucinol substitution pattern, Flavonoids are widely distributed in plants, fulfilling many functions. Flavonoids are the most important plant pigments for coloration, producing yellow or red/blue pigmentation in petals designed to attract pollinator animals. In higher plants, flavonoids are involved in UV filtration, symbiotic nitrogen fixation and they may also act as chemical messengers, physiological regulators, and cell cycle inhibitors. Flavonoids secreted by the root of their host plant help Rhizobia in the stage of their symbiotic relationship with legumes like peas, beans, clover. In addition, some flavonoids have inhibitory activity against organisms that cause plant diseases, over 5000 naturally occurring flavonoids have been characterized from various plants. Flavonols, the original such as quercetin, are also found ubiquitously. Further information on sources of flavonoids can be obtained from the US Department of Agriculture flavonoid database. Parsley, both fresh and dried, contains flavones, blueberries are a dietary source of anthocyanidins. Black tea is a source of dietary flavan-3-ols. The citrus flavonoids include hesperidin, quercitrin, rutin, and the flavone tangeritin, Flavonoids exist naturally in cocoa, but because they can be bitter, they are often removed from chocolate, even dark chocolate. Although flavonoids are present in milk chocolate, milk may interfere with their absorption, peanut skin contains significant polyphenol content, including flavonoids. Food composition data for flavonoids were provided by the USDA database on flavonoids, in the United States NHANES survey, mean flavonoid intake was 190 mg/d in adults, with flavan-3-ols as the main contributor. In the European Union, based on data from EFSA, mean flavonoid intake was 140 mg/d, the main type of flavonoids consumed in the EU and USA were flavan-3-ols, mainly from tea, while intake of other flavonoids was considerably lower
18.
Ehrlich's reagent
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Ehrlichs reagent or Ehrlich reagent is a reagent that contains p-dimethylaminobenzaldehyde and thus can act as an indicator to presumptively identify indoles and urobilinogen. Several Ehrlich tests use the reagent in a medical test, some are drug tests, a very common Ehrlich test is a simple spot test to identify possible psychoactive compounds such as tryptamines and ergoloids. The reagent will also give a result for opium, despite the opiates not containing the indole functional group. It is named after Nobel Prize winner Paul Ehrlich who used it to distinguish typhoid from simple diarrhoea. The reagent is prepared by dissolving 0. 5–2.0 g of p–dimethylaminobenzaldehyde in 50 mL of 95% ethanol and 50 mL of concentrated hydrochloric acid and is best used when fresh, Other alcohols, such as 1-propanol, can also be used as well. The Ehrlich reagent is similar to a number of other tests, The van Urk reagent, which uses DMAB, sulfuric acid. The Renz and Loew reagent, which uses p-dimethylaminocinnamaldehyde and may also be used for the detection of flavonoids, the improved hallucinogen reagent, which uses 5 g DMAB in 100 mL concentrated phosphoric acid and 100 mL of methanol. The Ehrlich reagent works by binding to the C2 position of two indole moieties to form a resonance stabilised carbenium ion compound, pill testing Other alkaloid spot tests, Froehde reagent Indole test Kovacs reagent, similar but uses isoamyl alcohol Liebermann reagent Marquis reagent
19.
PubMed Identifier
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PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval, from 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home-, the PubMed system was offered free to the public in June 1997, when MEDLINE searches via the Web were demonstrated, in a ceremony, by Vice President Al Gore. Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog. As of 5 January 2017, PubMed has more than 26.8 million records going back to 1966, selectively to the year 1865, and very selectively to 1809, about 500,000 new records are added each year. As of the date,13.1 million of PubMeds records are listed with their abstracts. In 2016, NLM changed the system so that publishers will be able to directly correct typos. Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMeds search window, when a journal article is indexed, numerous article parameters are extracted and stored as structured information. Such parameters are, Article Type, Secondary identifiers, Language, publication type parameter enables many special features. As these clinical girish can generate small sets of robust studies with considerable precision, since July 2005, the MEDLINE article indexing process extracts important identifiers from the article abstract and puts those in a field called Secondary Identifier. The secondary identifier field is to store numbers to various databases of molecular sequence data, gene expression or chemical compounds. For clinical trials, PubMed extracts trial IDs for the two largest trial registries, ClinicalTrials. gov and the International Standard Randomized Controlled Trial Number Register, a reference which is judged particularly relevant can be marked and related articles can be identified. If relevant, several studies can be selected and related articles to all of them can be generated using the Find related data option, the related articles are then listed in order of relatedness. To create these lists of related articles, PubMed compares words from the title and abstract of each citation, as well as the MeSH headings assigned, using a powerful word-weighted algorithm. The related articles function has been judged to be so precise that some researchers suggest it can be used instead of a full search, a strong feature of PubMed is its ability to automatically link to MeSH terms and subheadings. Examples would be, bad breath links to halitosis, heart attack to myocardial infarction, where appropriate, these MeSH terms are automatically expanded, that is, include more specific terms. Terms like nursing are automatically linked to Nursing or Nursing and this important feature makes PubMed searches automatically more sensitive and avoids false-negative hits by compensating for the diversity of medical terminology. The My NCBI area can be accessed from any computer with web-access, an earlier version of My NCBI was called PubMed Cubby
. PMID 18423367.