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
A topical medication is a medication that is applied to a particular place on or in the body, as opposed to systemically. Most often this means application to surfaces such as the skin or mucous membranes to treat ailments via a large range of classes including creams, gels, lotions. Many topical medications are epicutaneous, meaning that they are applied directly to the skin, as a route of administration, the topical route is contrasted with the enteral route, the intravenous route, and others. A topical effect, in the sense, may refer to a local, rather than systemic. However, many topically administered drugs have effects, because they reach the circulation after being absorbed by the tissues. Topical medications differ from other types of drugs because mishandling them can lead to certain complications in a patient or administrator of the drug. Some hydrophobic chemicals, such as hormones, can be absorbed into the body after being applied to the skin in the form of a cream, gel. Transdermal patches have become a means of administering some drugs for birth control, hormone replacement therapy.
One example of an antibiotic that may be applied topically is chloramphenicol, a medications potency often is changed with its base. For example, some topical steroids will be classified one or two strengths higher when moving from cream to ointment, as a rule of thumb, an ointment base is more occlusive and will drive the medication into the skin more rapidly than a solution or cream base. The manufacturer of each product has total control over the content of the base of a medication. Although containing the active ingredients, one manufacturers cream might be more acidic than the next. For example, a formulation of miconazole antifungal cream might irritate the skin less than an athlete foot formulation of miconazole cream. These variations can, on occasion, result in different clinical outcomes, no comparative potency labeling exists to ensure equal efficacy between brands of topical steroids. Studies have confirmed that the potency of some topical steroid products may differ according to manufacturer or brand, however, in a simple base like an ointment, much less variation between manufacturers is common.
In dermatology, the base of a medication is often as important as the medication itself. It is extremely important to receive a medication in the correct base, a pharmacist should not substitute an ointment for a cream, or vice versa, as the potency of the medication can change. As a result, what the manufacturers marketing department chooses to list on the label of a medication might be completely different from what the form would normally be called
Pharmacokinetics, sometimes abbreviated as PK, is a branch of pharmacology dedicated to determining the fate of substances administered to a living organism. The substances of interest include any chemical xenobiotic such as, pharmaceutical drugs, food additives, cosmetic ingredients, etc. It attempts to analyze chemical metabolism and to discover the fate of a chemical from the moment that it is administered up to the point at which it is eliminated from the body. Pharmacokinetics is the study of how an organism affects a drug, both together influence dosing and adverse effects, as seen in PK/PD models. Pharmacokinetic properties of chemicals are affected by the route of administration and these may affect the absorption rate. Models have been developed to simplify conceptualization of the processes that take place in the interaction between an organism and a chemical substance. The various compartments that the model is divided into are commonly referred to as the ADME scheme, absorption - the process of a substance entering the blood circulation.
Distribution - the dispersion or dissemination of substances throughout the fluids, metabolism – the recognition by the organism that a foreign substance is present and the irreversible transformation of parent compounds into daughter metabolites. Excretion - the removal of the substances from the body, in rare cases, some drugs irreversibly accumulate in body tissue. The two phases of metabolism and excretion can be grouped together under the title elimination, the study of these distinct phases involves the use and manipulation of basic concepts in order to understand the process dynamics. All these concepts can be represented through mathematical formulas that have a graphical representation. The model outputs for a drug can be used in industry or in the application of pharmacokinetic concepts. Clinical pharmacokinetics provides many performance guidelines for effective and efficient use of drugs for human-health professionals, in practice, it is generally considered that steady state is reached when a time of 4 to 5 times the half-life for a drug after regular dosing is started.
Noncompartmental methods estimate the exposure to a drug by estimating the area under the curve of a concentration-time graph, compartmental methods estimate the concentration-time graph using kinetic models. Noncompartmental methods are more versatile in that they do not assume any specific compartmental model. The final outcome of the transformations that a drug undergoes in an organism, a number of functional models have been developed in order to simplify the study of pharmacokinetics. These models are based on a consideration of an organism as a number of related compartments, the simplest idea is to think of an organism as only one homogenous compartment. However, these models do not always reflect the real situation within an organism
Enzymes /ˈɛnzaɪmz/ are macromolecular biological catalysts. Enzymes accelerate, or catalyze, chemical reactions, the molecules at the beginning of the process upon which enzymes may act are called substrates and the enzyme converts these into different molecules, called products. Almost all metabolic processes in the cell need enzymes in order to occur at rates fast enough to sustain life, the set of enzymes made in a cell determines which metabolic pathways occur in that cell. The study of enzymes is called enzymology, enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins, although a few are catalytic RNA molecules, enzymes specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the rate of a reaction by lowering its activation energy, some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example is orotidine 5-phosphate decarboxylase, which allows a reaction that would take millions of years to occur in milliseconds.
Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules, inhibitors are molecules that decrease enzyme activity, many drugs and poisons are enzyme inhibitors. An enzymes activity decreases markedly outside its optimal temperature and pH, some enzymes are used commercially, for example, in the synthesis of antibiotics. French chemist Anselme Payen was the first to discover an enzyme, diastase and he wrote that alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells. In 1877, German physiologist Wilhelm Kühne first used the term enzyme, the word enzyme was used to refer to nonliving substances such as pepsin, and the word ferment was used to refer to chemical activity produced by living organisms. Eduard Buchner submitted his first paper on the study of yeast extracts in 1897, in a series of experiments at the University of Berlin, he found that sugar was fermented by yeast extracts even when there were no living yeast cells in the mixture.
He named the enzyme that brought about the fermentation of sucrose zymase, in 1907, he received the Nobel Prize in Chemistry for his discovery of cell-free fermentation. Following Buchners example, enzymes are usually named according to the reaction they carry out, the biochemical identity of enzymes was still unknown in the early 1900s. Sumner showed that the enzyme urease was a protein and crystallized it. These three scientists were awarded the 1946 Nobel Prize in Chemistry, the discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. This high-resolution structure of lysozyme marked the beginning of the field of structural biology, an enzymes name is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase
Excretion is the process by which metabolic wastes and other non-useful materials are eliminated from an organism. In vertebrates this is carried out by the lungs, kidneys. This is in contrast with secretion, where the substance may have specific tasks after leaving the cell, excretion is an essential process in all forms of life. For example, in urine is expelled through the urethra. In unicellular organisms, waste products are discharged directly through the surface of the cell, green plants produce carbon dioxide and water as respiratory products. In green plants, the carbon dioxide released during respiration gets utilized during photosynthesis, oxygen is a by product generated during photosynthesis, and exits through stomata, root cell walls, and other routes. Plants can get rid of water by transpiration and guttation. These latter processes do not need added energy, they act passively, during the pre-abscission phase, the metabolic levels of a leaf are high. Plants excrete some waste substances into the soil around them, in animals, the main excretory products are carbon dioxide, urea, uric acid and creatine.
The liver and kidneys clear many substances from the blood, aquatic animals usually excrete ammonia directly into the external environment, as this compound has high solubility and there is ample water available for dilution. In terrestrial animals ammonia-like compounds are converted into other materials as there is less water in the environment. Birds excrete their nitrogenous wastes as uric acid in the form of a paste and this is metabolically more expensive, but allows more efficient water retention and it can be stored more easily in the egg. Many avian species, especially seabirds, can excrete salt via specialized nasal salt glands, in insects, a system involving Malpighian tubules is utilized to excrete metabolic waste. Metabolic waste diffuses or is actively transported into the tubule, which transports the wastes to the intestines, the metabolic waste is released from the body along with fecal matter. The excreted material may be called dejecta or ejecta, in pathology the word ejecta is more commonly used.
UAlberta. ca, Animation of excretion Brian J Ford on leaf fall in Nature
Simplified molecular-input line-entry system
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 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
In chemistry, an alcohol is any organic compound in which the hydroxyl functional group is bound to a saturated carbon atom. The term alcohol originally referred to the alcohol ethanol, the predominant alcohol in alcoholic beverages. The suffix -ol in non-systematic names typically indicates that the substance includes a functional group and, so. But many substances, particularly sugars contain hydroxyl functional groups without using the suffix, an important class of alcohols, of which methanol and ethanol are the simplest members is the saturated straight chain alcohols, the general formula for which is CnH2n+1OH. The word alcohol is from the Arabic kohl, a used as an eyeliner. Al- is the Arabic definite article, equivalent to the in English, alcohol was originally used for the very fine powder produced by the sublimation of the natural mineral stibnite to form antimony trisulfide Sb 2S3, hence the essence or spirit of this substance. It was used as an antiseptic and cosmetic, the meaning of alcohol was extended to distilled substances in general, and narrowed to ethanol, when spirits as a synonym for hard liquor.
Bartholomew Traheron, in his 1543 translation of John of Vigo, Vigo wrote, the barbarous auctours use alcohol, or alcofoll, for moost fine poudre. The 1657 Lexicon Chymicum, by William Johnson glosses the word as antimonium sive stibium, by extension, the word came to refer to any fluid obtained by distillation, including alcohol of wine, the distilled essence of wine. Libavius in Alchymia refers to vini alcohol vel vinum alcalisatum, Johnson glosses alcohol vini as quando omnis superfluitas vini a vino separatur, ita ut accensum ardeat donec totum consumatur, nihilque fæcum aut phlegmatis in fundo remaneat. The words meaning became restricted to spirit of wine in the 18th century and was extended to the class of substances so-called as alcohols in modern chemistry after 1850, the term ethanol was invented 1892, based on combining the word ethane with ol the last part of alcohol. In the IUPAC system, in naming simple alcohols, the name of the alkane chain loses the terminal e and adds ol, e. g. as in methanol and ethanol.
When necessary, the position of the group is indicated by a number between the alkane name and the ol, propan-1-ol for CH 3CH 2CH 2OH, propan-2-ol for CH 3CHCH3. If a higher priority group is present, the prefix hydroxy is used, in other less formal contexts, an alcohol is often called with the name of the corresponding alkyl group followed by the word alcohol, e. g. methyl alcohol, ethyl alcohol. Propyl alcohol may be n-propyl alcohol or isopropyl alcohol, depending on whether the group is bonded to the end or middle carbon on the straight propane chain. As described under systematic naming, if another group on the molecule takes priority, Alcohols are classified into primary and tertiary, based upon the number of carbon atoms connected to the carbon atom that bears the hydroxyl functional group. The primary alcohols have general formulas RCH2OH, the simplest primary alcohol is methanol, for which R=H, and the next is ethanol, for which R=CH3, the methyl group. Secondary alcohols are those of the form RRCHOH, the simplest of which is 2-propanol, for the tertiary alcohols the general form is RRRCOH
Propylene glycol, called propane-1, 2-diol, is a synthetic organic compound with the chemical formula C3H8O2. It is a colorless liquid which is nearly odorless but possesses a faintly sweet taste. Chemically it is classed as a diol and is miscible with a range of solvents, including water, acetone. The compound is sometimes called α-propylene glycol to distinguish it from the isomer propane-1, propylene glycol is a clear and hygroscopic liquid. Propylene glycol contains a carbon atom, so it exists in two enantiomers. The commercial product is a racemic mixture, pure optical isomers can be obtained by hydration of optically pure propylene oxide. The freezing point of water is depressed when mixed with propylene glycol owing to the effects of dissolution of a solute in a solvent. In general, glycols are non-corrosive, have low volatility and very low toxicity, however. Industrially, propylene glycol is produced from propylene oxide, and global capacity in 1990 was 900,000 tonnes per year, final products contain 20% propylene glycol,1. 5% of dipropylene glycol and small amounts of other polypropylene glycols.
Further purification produces finished industrial grade or USP/JP/EP/BP grade propylene glycol that is typically 99. 5% or greater, propylene glycol can be converted from glycerol, a biodiesel byproduct. This starting material is usually reserved for use because of the noticeable odor. In this regard, propylene glycol reacts with a mixture of unsaturated maleic anhydride and this partially unsaturated polymer undergoes further crosslinking to yield thermoset plastics. Related to this application, propylene glycol reacts with propylene oxide to give oligomers and polymers that are used to produce polyurethanes, propylene glycol is used as a humectant and preservative in food and for tobacco products. It is one of the ingredients, along with vegetable glycerin, of the e-liquid and cartridges used in electronic cigarettes. Propylene glycol is used in various edible items such as coffee-based drinks, liquid sweeteners, ice cream, whipped dairy products. Vaporizers used for delivery of pharmaceuticals or personal-care products often include propylene glycol among the ingredients, propylene glycol is used as a solvent in many pharmaceuticals, including oral and topical formulations, such as for diazepam and lorazepam which are insoluble in water.
Certain formulations of artificial tears, such as Systane, use proplyene glycol as an ingredient, like ethylene glycol, propylene glycol is able to lower the freezing point of water, and so it is used as aircraft de-icing fluid. Water-propylene glycol mixtures dyed pink to indicate the mixture is relatively nontoxic are sold under the name of RV or marine antifreeze, propylene glycol is frequently used as a substitute for ethylene glycol in low toxicity, environmentally friendly automotive antifreeze
Protein Data Bank
The Protein Data Bank is a crystallographic database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The PDB is overseen by a called the Worldwide Protein Data Bank. The PDB is a key resource in areas of structural biology, most major scientific journals, and some funding agencies, now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB, for example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology. By 1971, one of Meyers programs, SEARCH, enabled researchers to access information from the database to study protein structures offline. SEARCH was instrumental in enabling networking, thus marking the beginning of the PDB. Upon Hamiltons death in 1973, Tom Koeztle took over direction of the PDB for the subsequent 20 years, in January 1994, Joel Sussman of Israels Weizmann Institute of Science was appointed head of the PDB.
In October 1998, the PDB was transferred to the Research Collaboratory for Structural Bioinformatics, the new director was Helen M. Berman of Rutgers University. In 2003, with the formation of the wwPDB, the PDB became an international organization, the founding members are PDBe, RCSB, and PDBj. Each of the four members of wwPDB can act as deposition, data processing, the data processing refers to the fact that wwPDB staff review and annotate each submitted entry. The data are automatically checked for plausibility. The PDB database is updated weekly, the PDB holdings list is updated weekly. As of 14 March 2017, the breakdown of current holdings is as follows,103,514 structures in the PDB have a structure factor file,9,057 structures have an NMR restraint file. 2,826 structures in the PDB have a chemical shifts file, the final conformation of the protein is obtained, in the latter case, by solving a distance geometry problem. A few proteins are determined by cryo-electron microscopy, the significance of the structure factor files, mentioned above, is that, for PDB structures determined by X-ray diffraction that have a structure file, the electron density map may be viewed.
The data of such structures is stored on the electron density server, since 2007, the rate of accumulation of new protein structures appears to have plateaued. The file format used by the PDB was called the PDB file format. This original format was restricted by the width of computer punch cards to 80 characters per line, around 1996, the macromolecular Crystallographic Information file format, mmCIF, which is an extension of the CIF format started to be phased in
Necrosis is a form of cell injury which results in the premature death of cells in living tissue by autolysis. Necrosis is caused by external to the cell or tissue, such as infection, toxins. In contrast, apoptosis is a naturally occurring programmed and targeted cause of cellular death, while apoptosis often provides beneficial effects to the organism, necrosis is almost always detrimental and can be fatal. This initiates in the tissue a inflammatory response which attracts leukocytes. However, microbial damaging substances released by leukocytes would create collateral damage to surrounding tissues, too much collateral damage would inhibit the healing process. Thus, untreated necrosis results in a build-up of decomposing dead tissue, for this reason, it is often necessary to remove necrotic tissue surgically, a procedure known as debridement. Coagulation occurs as a result of protein denaturation, causing albumin to transform into a firm and this pattern of necrosis is typically seen in hypoxic environments, such as infarction.
Coagulative necrosis occurs primarily in tissues such as the kidney, severe ischemia most commonly causes necrosis of this form. Liquefactive necrosis, in contrast to necrosis, is characterized by the digestion of dead cells to form a viscous liquid mass. This is typical of bacterial, or sometimes fungal, infections because of their ability to stimulate an inflammatory response, the necrotic liquid mass is frequently creamy yellow due to the presence of dead leukocytes and is commonly known as pus. Gangrenous necrosis can be considered a type of coagulative necrosis that resembles mummified tissue and it is characteristic of ischemia of lower limb and the gastrointestinal tracts. The necrotic tissue appears as white and friable, like clumped cheese, dead cells disintegrate but are not completely digested, leaving granular particles. Microscopic examination shows amorphous granular debris enclosed within a distinctive inflammatory border, fat necrosis is specialized necrosis of fat tissue, resulting from the action of activated lipases on fatty tissues such as the pancreas.
Calcium, magnesium or sodium may bind to these lesions to produce a chalky-white substance, the calcium deposits are microscopically distinctive and may be large enough to be visible on radiographic examinations. To the naked eye, calcium deposits appear as gritty white flecks, fibrinoid necrosis is a special form of necrosis usually caused by immune-mediated vascular damage. It is marked by complexes of antigen and antibodies, sometimes referred to as “immune complexes” deposited within arterial walls together with fibrin, there are very specific forms of necrosis such as gangrene, gummatous necrosis and hemorrhagic necrosis. Some spider bites may lead to necrosis, in the United States, only spider bites from the brown recluse spider reliably progress to necrosis. In other countries, spiders of the genus, such as the Chilean recluse in South America, are known to cause necrosis