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.
ChEMBL
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ChEMBL or ChEMBLdb is a manually curated chemical database of bioactive molecules with drug-like properties. It is maintained by the European Bioinformatics Institute, of the European Molecular Biology Laboratory, based at the Wellcome Trust Genome Campus, Hinxton, the database, originally known as StARlite, was developed by a biotechnology company called Inpharmatica Ltd. later acquired by Galapagos NV. The data was acquired for EMBL in 2008 with an award from The Wellcome Trust, resulting in the creation of the ChEMBL chemogenomics group at EMBL-EBI, the ChEMBL database contains compound bioactivity data against drug targets. Bioactivity is reported in Ki, Kd, IC50, and EC50, data can be filtered and analyzed to develop compound screening libraries for lead identification during drug discovery. ChEMBL version 2 was launched in January 2010, including 2.4 million bioassay measurements covering 622,824 compounds and this was obtained from curating over 34,000 publications across twelve medicinal chemistry journals. ChEMBLs coverage of available bioactivity data has grown to become the most comprehensive ever seen in a public database, in October 2010 ChEMBL version 8 was launched, with over 2.97 million bioassay measurements covering 636,269 compounds. ChEMBL_10 saw the addition of the PubChem confirmatory assays, in order to integrate data that is comparable to the type, ChEMBLdb can be accessed via a web interface or downloaded by File Transfer Protocol. It is formatted in a manner amenable to computerized data mining, ChEMBL is also integrated into other large-scale chemistry resources, including PubChem and the ChemSpider system of the Royal Society of Chemistry. In addition to the database, the ChEMBL group have developed tools and these include Kinase SARfari, an integrated chemogenomics workbench focussed on kinases. The system incorporates and links sequence, structure, compounds and screening data, the primary purpose of ChEMBL-NTD is to provide a freely accessible and permanent archive and distribution centre for deposited data. July 2012 saw the release of a new data service, sponsored by the Medicines for Malaria Venture. The data in this service includes compounds from the Malaria Box screening set, myChEMBL, the ChEMBL virtual machine, was released in October 2013 to allow users to access a complete and free, easy-to-install cheminformatics infrastructure. In December 2013, the operations of the SureChem patent informatics database were transferred to EMBL-EBI, in a portmanteau, SureChem was renamed SureChEMBL. 2014 saw the introduction of the new resource ADME SARfari - a tool for predicting and comparing cross-species ADME targets
3.
ChemSpider
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ChemSpider is a database of chemicals. ChemSpider is owned by the Royal Society of Chemistry, the database contains information on more than 50 million molecules from over 500 data sources including, Each chemical is given a unique identifier, which forms part of a corresponding URL. This is an approach to develop an online chemistry database. The search can be used to widen or restrict already found results, structure searching on mobile devices can be done using free apps for iOS and for the Android. The ChemSpider database has been used in combination with text mining as the basis of document markup. The result is a system between chemistry documents and information look-up via ChemSpider into over 150 data sources. ChemSpider was acquired by the Royal Society of Chemistry in May,2009, prior to the acquisition by RSC, ChemSpider was controlled by a private corporation, ChemZoo Inc. The system was first launched in March 2007 in a release form. ChemSpider has expanded the generic support of a database to include support of the Wikipedia chemical structure collection via their WiChempedia implementation. A number of services are available online. SyntheticPages is an interactive database of synthetic chemistry procedures operated by the Royal Society of Chemistry. Users submit synthetic procedures which they have conducted themselves for publication on the site and these procedures may be original works, but they are more often based on literature reactions. Citations to the published procedure are made where appropriate. They are checked by an editor before posting. The pages do not undergo formal peer-review like a journal article. The comments are moderated by scientific editors. The intention is to collect practical experience of how to conduct useful chemical synthesis in the lab, while experimental methods published in an ordinary academic journal are listed formally and concisely, the procedures in ChemSpider SyntheticPages are given with more practical detail. Comments by submitters are included as well, other publications with comparable amounts of detail include Organic Syntheses and Inorganic Syntheses
4.
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
5.
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
6.
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
7.
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
8.
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
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.
GHS hazard pictograms
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Hazard pictograms form part of the international Globally Harmonized System of Classification and Labelling of Chemicals. Two sets of pictograms are included within the GHS, one for the labelling of containers and for workplace hazard warnings, either one or the other is chosen, depending on the target audience, but the two are not used together. The two sets of use the same symbols for the same hazards, although certain symbols are not required for transport pictograms. Transport pictograms come in variety of colors and may contain additional information such as a subcategory number. It has still to be implemented by the European Union in 2009, the following pictograms are included in the Worldwide Model Using but have not been incorporated into the GHS, ICZ and Catwallsh Hazcom Labelling because of the nature of the hazards. Globally Harmonized System of Classification and Labelling of Chemicals, New York and Geneva, United Nations,2007, ISBN 978-92-1-116957-7, ST/SG/AC. 10/30/Rev. Model Regulations, New York and Geneva, United Nations,2007, ISBN 978-92-1-139120-6, manual of Tests and Criteria, New York and Geneva, United Nations,2002, ISBN 92-1-139087-7, ST/SG/AC. 10/11/Rev.4 GHS pictogram gallery from the United Nations Economic Commission for Europe
13.
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
14.
Aromaticity
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Aromatic molecules are very stable, and do not break apart easily to react with other substances. Organic compounds that are not aromatic are classified as aliphatic compounds—they might be cyclic, since the most common aromatic compounds are derivatives of benzene, the word “aromatic” occasionally refers informally to benzene derivatives, and so it was first defined. Nevertheless, many aromatic compounds exist. In living organisms, for example, the most common aromatic rings are the bases in RNA and DNA. An aromatic functional group or other substituent is called an aryl group, the earliest use of the term aromatic was in an article by August Wilhelm Hofmann in 1855. Hofmann used the term for a class of compounds, many of which have odors. In terms of the nature of the molecule, aromaticity describes a conjugated system often made of alternating single and double bonds in a ring. This configuration allows for the electrons in the pi system to be delocalized around the ring, increasing the molecules stability. The molecule cannot be represented by one structure, but rather a hybrid of different structures. These molecules cannot be found in one of these representations, with the longer single bonds in one location. Rather, the molecule exhibits bond lengths in between those of single and double bonds and this commonly seen model of aromatic rings, namely the idea that benzene was formed from a six-membered carbon ring with alternating single and double bonds, was developed by August Kekulé. The model for benzene consists of two forms, which corresponds to the double and single bonds superimposing to produce six one-and-a-half bonds. Benzene is a stable molecule than would be expected without accounting for charge delocalization. As is standard for resonance diagrams, the use of an arrow indicates that two structures are not distinct entities but merely hypothetical possibilities. Neither is a representation of the actual compound, which is best represented by a hybrid of these structures. A C=C bond is shorter than a C−C bond, but benzene is perfectly hexagonal—all six carbon–carbon bonds have the same length, intermediate between that of a single and that of a double bond. In a cyclic molecule with three alternating double bonds, cyclohexatriene, the length of the single bond would be 1.54 Å. However, in a molecule of benzene, the length of each of the bonds is 1.40 Å, a better representation is that of the circular π-bond, in which the electron density is evenly distributed through a π-bond above and below the ring
15.
Refractive index
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In optics, the refractive index or index of refraction n of a material is a dimensionless number that describes how light propagates through that medium. It is defined as n = c v, where c is the speed of light in vacuum, for example, the refractive index of water is 1.333, meaning that light travels 1.333 times faster in a vacuum than it does in water. The refractive index determines how light is bent, or refracted. The refractive indices also determine the amount of light that is reflected when reaching the interface, as well as the angle for total internal reflection. This implies that vacuum has a index of 1. The refractive index varies with the wavelength of light and this is called dispersion and causes the splitting of white light into its constituent colors in prisms and rainbows, and chromatic aberration in lenses. Light propagation in absorbing materials can be described using a refractive index. The imaginary part then handles the attenuation, while the real part accounts for refraction, the concept of refractive index is widely used within the full electromagnetic spectrum, from X-rays to radio waves. It can also be used with wave phenomena such as sound, in this case the speed of sound is used instead of that of light and a reference medium other than vacuum must be chosen. Thomas Young was presumably the person who first used, and invented, at the same time he changed this value of refractive power into a single number, instead of the traditional ratio of two numbers. The ratio had the disadvantage of different appearances, newton, who called it the proportion of the sines of incidence and refraction, wrote it as a ratio of two numbers, like 529 to 396. Hauksbee, who called it the ratio of refraction, wrote it as a ratio with a fixed numerator, hutton wrote it as a ratio with a fixed denominator, like 1.3358 to 1. Young did not use a symbol for the index of refraction, in the next years, others started using different symbols, n, m, and µ. For visible light most transparent media have refractive indices between 1 and 2, a few examples are given in the adjacent table. These values are measured at the yellow doublet D-line of sodium, with a wavelength of 589 nanometers, gases at atmospheric pressure have refractive indices close to 1 because of their low density. Almost all solids and liquids have refractive indices above 1.3, aerogel is a very low density solid that can be produced with refractive index in the range from 1.002 to 1.265. Moissanite lies at the end of the range with a refractive index as high as 2.65. Most plastics have refractive indices in the range from 1.3 to 1.7, for infrared light refractive indices can be considerably higher
16.
Naphthalene
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Naphthalene is an organic compound with formula C 10H8. It is the simplest polycyclic aromatic hydrocarbon, and is a crystalline solid with a characteristic odor that is detectable at concentrations as low as 0.08 ppm by mass. As an aromatic hydrocarbon, naphthalenes structure consists of a pair of benzene rings. It is best known as the ingredient of traditional mothballs. In the early 1820s, two separate reports described a white solid with a pungent odor derived from the distillation of coal tar, in 1821, John Kidd cited these two disclosures and then described many of this substances properties and the means of its production. He proposed the name naphthaline, as it had been derived from a kind of naphtha, naphthalenes chemical formula was determined by Michael Faraday in 1826. The structure of two fused benzene rings was proposed by Emil Erlenmeyer in 1866, and confirmed by Carl Gräbe three years later, a naphthalene molecule can be viewed as the fusion of a pair of benzene rings. As such, naphthalene is classified as a polycyclic aromatic hydrocarbon. There are two sets of equivalent hydrogen atoms, the positions are numbered 1,4,5, and 8, and the beta positions,2,3,6. Unlike benzene, the bonds in naphthalene are not of the same length. The bonds C1−C2, C3−C4, C5−C6 and C7−C8 are about 1.37 Å in length and this difference, established by X-ray diffraction, is consistent with the valence bond model in naphthalene and in particular, with the theorem of cross-conjugation. This theorem would describe naphthalene as an aromatic benzene unit bonded to a diene, as such, naphthalene possesses several resonance structures. Two isomers are possible for mono-substituted naphthalenes, corresponding to substitution at an alpha or beta position, bicyclodecapentaene is a structural isomer with a fused 4–8 ring system. In electrophilic aromatic substitution reactions, naphthalene reacts more readily than benzene, for example, chlorination and bromination of naphthalene proceeds without a catalyst to give 1-chloronaphthalene and 1-bromonaphthalene, respectively. In terms of regiochemistry, electrophiles attack occurs at the alpha position, for beta substitution, the intermediate has only six resonance structures, and only two of these are aromatic. Sulfonation, however, gives a mixture of the alpha product 1-naphthalenesulfonic acid, the 1-isomer forms predominantly at 25 °C, and the 2-isomer at 160 °C. Sulfonation to give the 1- and 2-sulfonic acid occurs readily, H 2SO4 + C 10H8 → C 10H 7−SO 3H + H 2O Further sulfonation occurs to give di-, tri- and these 1, 8-dilithio derivatives are precursors to a host of peri-naphthalene derivatives. With alkali metals, naphthalene forms the dark blue-green radical anion salts such as sodium naphthalenide, the naphthalenide salts are strong reducing agents
17.
Organochloride
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The chloroalkane class provides common examples. The wide structural variety and divergent chemical properties of lead to a broad range of names. Organochlorides are very useful compounds in many applications, but some are of profound environmental concern, chlorination modifies the physical properties of hydrocarbons in several ways. The compounds are typically denser than water due to the atomic weight of chlorine versus hydrogen. Aliphatic organochlorides are alkylating agents because chloride is a leaving group, many organochlorine compounds have been isolated from natural sources ranging from bacteria to humans. Chlorinated organic compounds are found in every class of biomolecules including alkaloids, terpenes, amino acids, flavonoids, steroids. In addition, a variety of simple chlorinated hydrocarbons including dichloromethane, chloroform, a majority of the chloromethane in the environment is produced naturally by biological decomposition, forest fires, and volcanoes. The natural organochloride epibatidine, an alkaloid isolated from tree frogs, has potent analgesic effects and has stimulated research into new pain medication, alkanes and aryl alkanes may be chlorinated under free radical conditions, with UV light. However, the extent of chlorination is difficult to control, aryl chlorides may be prepared by the Friedel-Crafts halogenation, using chlorine and a Lewis acid catalyst. The haloform reaction, using chlorine and sodium hydroxide, is able to generate alkyl halides from methyl ketones. Chlorine adds to the bonds on alkenes and alkynes as well. Alkenes react with chloride to give alkyl chlorides. Secondary and tertiary alcohols react with chloride to give the corresponding chlorides. Alternatively, the Appel reaction can be used, Alkyl chlorides are versatile building blocks in organic chemistry, while alkyl bromides and iodides are more reactive, alkyl chlorides tend to be less expensive and more readily available. Alkyl chlorides readily undergo attack by nucleophiles, heating alkyl halides with sodium hydroxide or water gives alcohols. Reaction with alkoxides or aroxides give ethers in the Williamson ether synthesis, Alkyl chlorides readily react with amines to give substituted amines. Alkyl chlorides are substituted by softer halides such as the iodide in the Finkelstein reaction, reaction with other pseudohalides such as azide, cyanide, and thiocyanate are possible as well. In the presence of a base, alkyl chlorides undergo dehydrohalogenation to give alkenes or alkynes
18.
Insecticide
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An insecticide is a substance used to kill insects. They include ovicides and larvicides used against insect eggs and larvae, Insecticides are used in agriculture, medicine, industry and by consumers. Insecticides are claimed to be a factor behind the increase in agricultural 20th centurys productivity. Nearly all insecticides have the potential to significantly alter ecosystems, many are toxic to humans, Insecticides can be classified in two major groups, systemic insecticides, which have residual or long term activity, and contact insecticides, which have no residual activity. Furthermore, one can distinguish three types of insecticide, natural insecticides, such as nicotine, pyrethrum and neem extracts, made by plants as defenses against insects. Organic insecticides, which are chemical compounds, mostly working by contact. The mode of action describes how the pesticide kills or inactivates a pest and it provides another way of classifying insecticides. Mode of action is important in understanding whether an insecticide will be toxic to unrelated species, such as fish, birds, Insecticides are distinct from insect repellents, which do not kill. Systemic insecticides become incorporated and distributed throughout the whole plant. When insects feed on the plant, they ingest the insecticide, systemic insecticides produced by transgenic plants are called plant-incorporated protectants. For instance, a gene that codes for a specific Bacillus thuringiensis biocidal protein was introduced into corn, the plant manufactures the protein, which kills the insect when consumed. Contact insecticides are toxic to insects upon direct contact and these can be inorganic insecticides, which are metals and include arsenates, copper and fluorine compounds, which are less commonly used, and the commonly used sulfur. Contact insecticides can be organic insecticides, i. e. organic chemical compounds, synthetically produced, or they can be natural compounds like pyrethrum, neem oil etc. Contact insecticides usually have no residual activity, efficacy can be related to the quality of pesticide application, with small droplets, such as aerosols often improving performance. Many organic compounds are produced by plants for the purpose of defending the host plant from predation, a trivial case is tree rosin, which is a natural insecticide. Specific, the production of oleoresin by conifer species is a component of the response against insect attack. Many fragrances, e. g. oil of wintergreen, are in fact antifeedants, the technique has been expanded to include the use of RNA interference RNAi that fatally silences crucial insect genes. RNAi likely evolved as a defense against viruses, midgut cells in many larvae take up the molecules and help spread the signal
19.
Fungicide
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Fungicides are biocidal chemical compounds or biological organisms used to kill fungi or fungal spores. Fungi can cause damage in agriculture, resulting in critical losses of yield, quality. Fungicides are used both in agriculture and to fight fungal infections in animals, chemicals used to control oomycetes, which are not fungi, are also referred to as fungicides, as oomycetes use the same mechanisms as fungi to infect plants. Fungicides can either be contact, translaminar or systemic, contact fungicides are not taken up into the plant tissue and protect only the plant where the spray is deposited. Translaminar fungicides redistribute the fungicide from the upper, sprayed leaf surface to the lower, systemic fungicides are taken up and redistributed through the xylem vessels. Few fungicides move to all parts of a plant, some are locally systemic, and some move upwardly. Most fungicides that can be bought retail are sold in a liquid form, a very common active ingredient is sulfur, present at 0. 08% in weaker concentrates, and as high as 0. 5% for more potent fungicides. Fungicides in powdered form are usually around 90% sulfur and are very toxic, other active ingredients in fungicides include neem oil, rosemary oil, jojoba oil, the bacterium Bacillus subtilis, and the beneficial fungus Ulocladium oudemansii. Fungicide residues have been found on food for consumption, mostly from post-harvest treatments. Some fungicides are dangerous to health, such as vinclozolin. Ziram is also a fungicide that is thought to be toxic to humans if exposed to chronically, a number of fungicides are also used in human health care. Plants and other organisms have chemical defenses that give them an advantage against microorganisms such as fungi, in the field several mechanisms of resistance have been identified. The evolution of resistance can be gradual or sudden. In qualitative or discrete resistance, a mutation produces a race of a fungus with a degree of resistance. Such resistant varieties also tend to show stability, persisting after the fungicide has been removed from the market, for example, sugar beet leaf blotch remains resistant to azoles years after they were no longer used for control of the disease. This is because such mutations often have a selection pressure when the fungicide is used. In instances where resistance occurs more gradually, a shift in sensitivity in the pathogen to the fungicide can be seen, such resistance is polygenic – an accumulation of many mutations in different genes, each having a small additive effect. This type of resistance is known as quantitative or continuous resistance, in this kind of resistance, the pathogen population will revert to a sensitive state if the fungicide is no longer applied
20.
Chlordane
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The name Chlordane, or chlordan, is commonly used as both a specific chemical and as a mixture of compounds. This mixture, more specifically called technical chlordane, was first produced in the 1940s by Julius Hyman, technical chlordane development was by chance, during a search for possible uses of a by-product of synthetic rubber manufacturing. By chlorinating this by-product, persistent and potent insecticides were easily and cheaply produced. The chlorine atoms,7 in the case of heptachlor and 8 in chlordane, other members of the cyclodiene family of organochorine insecticides are aldrin and its epoxide, dieldrin, as well as endrin, which is a stereoisomer of dieldrin. In the United States, chlordane was used until 1988 as an insecticide for treating approximately 30 million homes for termites, for food crops like corn and citrus, technical grade chlordane is a complex mixture of over 120 structurally related chemical compounds. Chlordane is one so-called cyclodiene pesticide, meaning that it is derived from hexachlorocyclopentadiene, the β-isomer is popularly known as gamma and is more bioactive. The mixture that is composed of 147 components is called technical chlordane, Chlordane appears as a white or off-white crystals when synthesized, but it was more commonly sold in various formulations as oil solutions, emulsions, sprays, dusts, and powders. These products were sold in the United States from 1948 to 1988, because of concern about damage to the environment and harm to human health, the United States Environmental Protection Agency banned all uses of chlordane in 1983, except termite control. The EPA banned all uses of chlordane in 1988, the EPA recommends that children should not drink water with more than 60 parts of chlordane per billion parts of drinking water for longer than 1 day. EPA has set a limit in drinking water of 2 ppb, Chlordane is very persistent in the environment because it does not break down easily. It has an environmental half-life of 10 to 20 years, in the years 1948–1988 chlordane was a common pesticide for corn and citrus crops, as well as a method of home termite control. The United States Environmental Protection Agency reported that over 30 million homes were treated with technical chlordane or technical chlordane with heptachlor. Depending on the site of home treatment, the indoor air levels of chlordane can still exceed the Minimal Risks Levels for both cancer and chronic disease by orders of magnitude, Chlordane is excreted slowly through feces, urine elimination, and through breast milk in nursing mothers. It is able to cross the placenta and become absorbed by developing fetuses in pregnant women, a breakdown product of chlordane, the metabolite oxychlordane, accumulates in blood and adipose tissue with age. Being hydrophobic, chlordane adheres to soil particles and enters groundwater only slowly and it requires many years to degrade. It is highly toxic to fish, with an LD50 of 0. 022–0.095 mg/kg, trans-Nonachlor is more toxic than technical chlordane and cis-nonachlor is less toxic. Chlordane is a persistent organic pollutants, classified among the dirty dozen. No human epidemiological study has been conducted to determine the relationship between levels of chlordane/heptachlor in indoor air and rates of cancer in inhabitants, breathing chlordane in indoor air is the main route of exposure for these levels in human tissues
21.
Sigma Aldrich
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Sigma-Aldrich Corporation is an American chemical, life science and biotechnology company owned by Merck KGaA. The company is headquartered in St. Louis and has operations in approximately 40 countries, in September 2014, the German company Merck KGaA announced that it would be acquiring Sigma-Aldrich for 17.0 billion dollars. The acquisition was completed in November 2015 and Sigma-Aldrich became a subsidiary of Merck KGaA, the company is currently a part of Mercks life science business and in combination with Mercks earlier acquired Millipore, operates as MilliporeSigma. Sigma Chemical Company of St Louis and Aldrich Chemical Company of Milwaukee were both American specialty chemical companies when they merged in August 1975, the company grew throughout the 80s and 90s, with significant expansion in facilities, acquisitions and diversification into new market sectors. 1935 – Midwest Consultants was founded in St Louis by the Fischer brothers,1946 – Sigma was formed from Midwest Consultants and manufactured just adenosine triphosphate. They were the first to manufacture pure ATP,1972 – Sigmas IPO1951 – Aldrich founded in Milwaukee by Alfred Bader and Jack Eisendrath and manufactured just 1-methyl-3-nitro-1-nitrosoguanidine. 1966 – Aldrichs IPO1972 – Subsidiary Aldrich-Boranes launched to manufacture hydroboration products 1975 – Merger of Sigma Chemical and their first year earned $43 million in sales. 1999 – Sigma-Aldrich reaches $1 billion in sales 2005 – Announced membership in The RNAi Consortium 2014 – Merck KGaA announced that it would purchase Sigma-Aldrich for approx. 1978 – Makor Chemicals 1984 – Pathfinder 1986 – Bio Yeda, BioReliance, BioReliance had previously been acquired by Invitrogen and subsequently sold to Avista Capital Partners. 2014 – Cell Marque Key numbers for Sigma-Aldrich, research Specialties – Specialty analytical, biochemical and chemical products. Research Essentials – Commonly used laboratory chemicals and supplies, SAFC – Development and manufacturing services to the pharmaceutical, biopharmaceutical and diagnostic sectors. Aldrich is a supplier in the research and fine chemicals market, Aldrich provides organic and inorganic chemicals, building blocks, reagents, advanced materials and stable isotopes for chemical synthesis, medicinal chemistry and materials science. Aldrichs chemicals catalog, the Aldrich Catalog and Handbook is often used as a due to the inclusion of structures, physical data. Sigma RBI produces specialized products for use in the field of cell signaling, Fluka manufactures chemicals and reagents for analytical, organic and biochemical research, and intermediates for the chemical and pharmaceutical industries. Riedel-de Haën was incorporated with Sigma-Aldrich in 1999 and manufactures reagents, supelco is the chromatography products branch of Sigma-Aldrich. Sigma Life Science provides products such as custom DNA/RNA oligos, custom DNA and LNA probes, siRNA, isotopically-labelled peptides, Sigma Advanced Genetic Engineering Labs is a division within Sigma-Aldrich that specializes in genetic manipulation of in vivo systems for special research and development applications. It was formed in 2008 to investigate zinc finger nuclease technology, located in St. Louis, Missouri, SAGE Labs have developed knockout rats for the study of human diseases and disorders, which are sold for up to US$95,000. SAGE also announced its first successful effort in creating a knockout rabbit and its facilities include a specific pathogen free, biosecure vivarium as well as research and development labs
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