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, the database, originally known as StARlite, was developed by a biotechnology company called Inpharmatica Ltd. 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 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 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
1, 4-Dioxane is a heterocyclic organic compound, classified as an ether. It is a liquid with a faint sweet odor similar to that of diethyl ether. The compound is called simply dioxane because the other dioxane isomers are rarely encountered. Dioxane is used as a solvent for a variety of applications as well as in the laboratory. Dioxane is produced by the dehydration of diethylene glycol, which in turn is obtained from the hydrolysis of ethylene oxide. In 1985, the production capacity for dioxane was between 11,000 and 14,000 tons. In 1990, the total U. S. production volume of dioxane was between 5,250 and 9,150 tons, the dioxane molecule is centrosymmetric, meaning that it adopts a chair conformation, typical of relatives of cyclohexane. However, the molecule is conformationally flexible, and the conformation is easily adopted. In the 1980s, most of the produced was used as a stabilizer for 1,1, 1-trichloroethane for storage. Dioxane poisons this catalysis reaction by forming an adduct with aluminum trichloride, Dioxane is used in a variety of applications as a versatile aprotic solvent, e. g. for inks and cellulose esters.
It is substituted for tetrahydrofuran in some processes, because of its lower toxicity, while diethyl ether is rather insoluble in water, dioxane is miscible and in fact is hygroscopic. At standard pressure, the mixture of water and dioxane in the ratio 17.9,82.1 by mass is an azeotrope that boils at 87.6 C. The oxygen atoms are Lewis basic, and so dioxane is able to solvate many inorganic compounds and it reacts with Grignard reagents to precipitate the magnesium dihalide. In this way, dioxane is used to drive the Schlenk equilibrium, dimethylmagnesium is prepared in this manner,2 CH3MgBr +2 → MgBr22 + 2Mg Dioxane is used as an internal standard for proton NMR spectroscopy in D2O. Dioxane has an LD50 of 5170 mg/kg in rats and this compound is irritating to the eyes and respiratory tract. Exposure may cause damage to the nervous system, liver. In a 1978 mortality study conducted on workers exposed to 1, 4-Dioxane, Dioxane is classified by the National Toxicology Program as reasonably anticipated to be a human carcinogen.
It is classified by the IARC as a Group 2B carcinogen, the U. S. Environmental Protection Agency classifies dioxane as a probable human carcinogen, and a known irritant at concentrations significantly higher than those found in commercial products
Photochemistry is the branch of chemistry concerned with the chemical effects of light. Generally, this term is used to describe a chemical reaction caused by absorption of ultraviolet, in nature, photochemistry is of immense importance as it is the basis of photosynthesis and the formation of vitamin D with sunlight. Photochemical reactions proceed differently than temperature-driven reactions, photochemistry is destructive, as illustrated by the photodegradation of plastics. Photoexcitation is the first step in a process where the reactant is elevated to a state of higher energy. The first law of photochemistry, known as the Grotthuss–Draper law, when a molecule in the ground state absorbs light, one electron is excited to a higher orbital level. This electron maintains its spin according to the selection rule. The excitation to a singlet state can be from HOMO to LUMO or to a higher orbital, so that singlet excitation states S1, S2. Kashas rule stipulates that higher singlet states would quickly relax by radiationless decay or internal conversion to S1, thus, S1 is usually, but not always, the only relevant singlet excited state.
This excited state S1 can further relax to S0 by IC, but by an allowed radiative transition from S1 to S0 that emits a photon, this process is called fluorescence. Alternatively, it is possible for the excited state S1 to undergo spin inversion and this violation of the spin selection rule is possible by intersystem crossing of the vibrational and electronic levels of S1 and T1. According to Hunds rule of multiplicity, this T1 state would be somewhat more stable than S1. This triplet state can relax to the ground state S0 by radiationless IC or by a pathway called phosphorescence. This process implies a change of spin, which is forbidden by spin selection rules. Thus, triplet states generally have longer lifetimes than singlet states and these transitions are usually summarized in a state energy diagram or Jablonski diagram, the paradigm of molecular photochemistry. These excited species, either S1 or T1, have a half empty low-energy orbital, but at the same time, they have an electron in a high energy orbital, and are thus more reducing.
In general, excited species are prone to participate in electron transfer processes, Photochemical reactions require a light source that emits wavelengths corresponding to an electronic transition in the reactant. In the early experiments, sunlight was the source, although it is polychromatic. Mercury-vapor lamps are common in the laboratory
The structural formula of a chemical compound is a graphic representation of the molecular structure, showing how the atoms are arranged. The chemical bonding within the molecule is shown, either explicitly or implicitly. For example, many compounds exist in different isomeric forms. A structural formula is able to indicate arrangements of atoms in three dimensional space in a way that a formula may not be able to do. Several systematic chemical naming formats, as in chemical databases, are used that are equivalent to and these chemical nomenclature systems include SMILES, InChI and CML. Lewis structures are flat graphical formulas that show atom connectivity and lone pair or unpaired electrons and this notation is mostly used for small molecules. Each line represents the two electrons of a single bond, two or three parallel lines between pairs of atoms represent double or triple bonds, respectively. Alternatively, pairs of dots may be used to represent bonding pairs, in addition, all non-bonded electrons and any formal charges on atoms are indicated.
In early organic-chemistry publications, where use of graphics was strongly limited, skeletal formulas are the standard notation for more complex organic molecules. Hydrogen atoms attached to carbon atoms are not indicated, each atom is understood to be associated with enough hydrogen atoms to give the carbon atom four bonds. The presence of a positive or negative charge at a carbon atom takes the place of one of the hydrogen atoms. Hydrogen atoms attached to other than carbon must be written explicitly. Several methods exist to picture the three-dimensional arrangement of atoms in a molecule, chirality in skeletal formulas is indicated by the Natta projection method. Solid or dashed wedged bonds represent bonds pointing above-the-plane or below-the-plane of the paper, wavy single bonds represent unknown or unspecified stereochemistry or a mixture of isomers. For example, the adjacent diagram shows the fructose molecule with a bond to the HOCH2- group at the left. In this case the two ring structures are in chemical equilibrium with each other and with the open-chain structure.
The ring continually opens and closes, sometimes closing with one stereochemistry, skeletal formulae can depict cis and trans isomers of alkenes. Wavy single bonds are the way to represent unknown or unspecified stereochemistry or a mixture of isomers
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 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, 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
Safety data sheet
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 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
A single chiral atom or similar structural feature in a compound causes that compound to have two possible structures which are non-superposable, each a mirror image of the other. Each member of the pair is termed an enantiomorph, the property is termed enantiomerism. The presence of multiple features in a given compound increases the number of geometric forms possible. Enantiopure compounds refer to samples having, within the limits of detection and they are sometimes called optical isomers for this reason. Enantiomer members often have different chemical reactions with other enantiomer substances, since many biological molecules are enantiomers, there is sometimes a marked difference in the effects of two enantiomers on biological organisms. Owing to this discovery, drugs composed of one enantiomer can be developed to enhance the pharmacological efficacy. An example is eszopiclone, which is enantiopure and therefore administered in doses that are exactly 1/2 of the older, in the case of eszopiclone, the S enantiomer is responsible for all the desired effects, while the other enantiomer seems to be inactive. A dose of 2 mg of zopiclone must be administered to produce the therapeutic effect as 1 mg of eszopiclone.
In chemical synthesis of enantiomeric substances, non-enantiomeric precursors inevitably produce racemic mixtures, in the absence of an effective enantiomeric environment, separation of a racemic mixture into its enantiomeric components is impossible. The R/S system is an important nomenclature system for denoting distinct enantiomers, another system is based on prefix notation for optical activity, - and - or d- and l-. The Latin for left and right is laevus and dexter, respectively and right have always had moral connotations, and the Latin words for these are sinister and rectus. The English word right is a cognate of rectus and this is the origin of the D, L and S, R notations, and the employment of prefixes levo- and dextro- in common names. Most compounds that one or more asymmetric carbon atoms show enantiomerism. There are a few compounds that do have asymmetric carbon atoms. An example of such an enantiomer is the sedative thalidomide, which was sold in a number of countries across the world from 1957 until 1961 and it was withdrawn from the market when it was found to cause of birth defects.
One enantiomer caused the desirable effects, while the other, unavoidably present in equal quantities. The herbicide mecoprop is a mixture, with the --enantiomer possessing the herbicidal activity. Another example is the antidepressant drugs escitalopram and citalopram, citalopram is a racemate, escitalopram is a pure enantiomer
Ethylene is a hydrocarbon which has the formula C 2H4 or H2C=CH2. It is a flammable gas with a faint sweet and musky odour when pure. Ethylene is widely used in the industry, and its worldwide production exceeds that of any other organic compound. Much of this production goes toward polyethylene, a used plastic containing polymer chains of ethylene units in various chain lengths. Ethylene is an important natural plant hormone, used in agriculture to force the ripening of fruits and this hydrocarbon has four hydrogen atoms bound to a pair of carbon atoms that are connected by a double bond. All six atoms that comprise ethylene are coplanar, the H-C-H angle is 117. 4°, close to the 120° for ideal sp² hybridized carbon. The molecule is relatively rigid, rotation about the C-C bond is a high energy process that requires breaking the π-bond. The π-bond in the molecule is responsible for its useful reactivity. The double bond is a region of high density, thus it is susceptible to attack by electrophiles.
Many reactions of ethylene are catalyzed by metals, which bind transiently to the ethylene using both the π and π* orbitals. Being a simple molecule, ethylene is spectroscopically simple and its UV-vis spectrum is still used as a test of theoretical methods. In the United States and Europe, approximately 90% of ethylene is used to produce ethylene oxide, ethylene dichloride, most of the reactions with ethylene are electrophilic addition. Polyethylene consumes more than half of the worlds ethylene supply, called polyethene, is the worlds most widely used plastic. It is primarily used to make films in packaging, carrier bags, linear alpha-olefins, produced by oligomerization are used as precursors, plasticisers, synthetic lubricants, and as co-monomers in the production of polyethylenes. Ethylene is oxidized to ethylene oxide, a key raw material in the production of surfactants and detergents by ethoxylation. Ethylene oxide is hydrolyzed to produce ethylene glycol, widely used as an automotive antifreeze as well as higher molecular weight glycols, glycol ethers.
Ethylene undergoes oxidation by palladium to give acetaldehyde and this conversion remains a major industrial process. The process proceeds via the initial complexation of ethylene to a Pd center, major intermediates from the halogenation and hydrohalogenation of ethylene include ethylene dichloride, ethyl chloride and ethylene dibromide
An epoxide is a cyclic ether with a three-atom ring. This ring approximates an equilateral triangle, which makes it strained and they are produced on a large scale for many applications. In general, low molecular weight epoxides are colourless and nonpolar, a compound containing the epoxide functional group can be called an epoxy, epoxide and ethoxyline. Simple epoxides are often referred to as oxides, the epoxide of ethylene is ethylene oxide. Many compounds have trivial names, ethylene oxide is called oxirane, some names emphasize the presence of the epoxide functional group, as in the compound 1, 2-epoxycycloheptane, which can be called 1, 2-heptene oxide. A polymer formed from epoxide precursors is called an epoxy, the dominant epoxides industrially are ethylene oxide and propylene oxide, which are produced respectively on the scales of approximately 15 and 3 million tonnes/year. Other alkenes fail to react usefully, even propylene, many epoxides are generated by treating alkenes with peroxide-containing reagents, which donate a single oxygen atom.
Outside of the scale, the main challenge with this approach is that typical peroxides are more valuable than the product epoxides. For this reason, this methodology is restricted to fine chemical applications, metal complexes are useful catalysts for these reactions. Typical peroxide reagents include hydrogen peroxide, peroxycarboxylic acids, and alkyl hydroperoxides, in specialized applications, other peroxide-containing reagents are employed, such as dimethyldioxirane. Depending on the mechanism of the reaction and the geometry of the starting material. In addition, if there are other stereocenters present in the starting material, the metal-catalyzed epoxidation was first explored using tert-butyl hydroperoxide as a source of an O atom. Association of TBHP with the metal generates the active metal catalyst with a peroxy ligand and this approach is used for the production of propylene oxide from propylene using various catalysts. Both t-butyl hydroperoxide or ethylbenzene hydroperoxide can be used as oxygen sources, more typically for laboratory operations, the Prilezhaev reaction is employed.
This approach involves the oxidation of the alkene with a such as m-CPBA. Illustrative is the epoxidation of styrene with perbenzoic acid to styrene oxide, the peroxide is viewed as an electrophile, and the alkene a nucleophile. The reaction is considered to be concerted. The butterfly mechanism allows ideal positioning of the O-O sigma star orbital for C-C Pi electrons to attack, hydroperoxides are employed in catalytic enantioselective epoxidations, such as the Sharpless epoxidation and the Jacobsen epoxidation. Together with the Shi epoxidation, these reactions are useful for the synthesis of chiral epoxides
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 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