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.
IUPHAR/BPS
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The IUPHAR/BPS Guide to PHARMACOLOGY is an open-access website, acting as a portal to information on the biological targets of licensed drugs and other small molecules. The Guide to PHARMACOLOGY is developed as a joint venture between the International Union of Basic and Clinical Pharmacology and the British Pharmacological Society and this replaces and expands upon the original 2009 IUPHAR Database. The information featured includes pharmacological data, target and gene nomenclature, overviews and commentaries on each target family are included, with links to key references. The Guide to PHARMACOLOGY was initially made available online in December 2011 with additional material released in July 2012 and its network of over 700 specialist advisors contribute expertise and data. The current PI and Grant holder of the GtoPdb project is Prof. Jamie A. Davies, the development and release of the first version of the GtoPdb in 2012 was described in an editorial published in the British Journal of Pharmacology entitled Guide to Pharmacology. org- an update. The IUPHAR-DB is no longer being developed and all the contained within this site is now available through the Guide to PHARMACOLOGY. A complete list of all the approved drugs included on the website is available via the ligand list. The Guide to PHARMACOLOGY is being expanded to include information on targets and ligands. Search features on the website include quick and advanced search options, other features include Hot topic news items and a recent receptor-ligand pairing list. A hard copy summary of the database is published as The Concise Guide to Pharmacology 2015/2016 as a series of papers as a bi-annual supplement to the British Journal of Pharmacology. The Guide to PHARMACOLOGY includes links to other relevant resources via target, many of these resources maintain reciprocal links with the relevant Guide to PHARMACOLOGY pages. As of November 2015 the Wellcome Trust is supporting a new project to develop the Guide to Immumopharmacology, the latter continues to be supported by the British Pharmacological Society
6.
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
7.
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
8.
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
9.
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
10.
Density
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The density, or more precisely, the volumetric mass density, of a substance is its mass per unit volume. The symbol most often used for density is ρ, although the Latin letter D can also be used. Mathematically, density is defined as mass divided by volume, ρ = m V, where ρ is the density, m is the mass, and V is the volume. In some cases, density is defined as its weight per unit volume. For a pure substance the density has the numerical value as its mass concentration. Different materials usually have different densities, and density may be relevant to buoyancy, purity, osmium and iridium are the densest known elements at standard conditions for temperature and pressure but certain chemical compounds may be denser. Thus a relative density less than one means that the floats in water. The density of a material varies with temperature and pressure and this variation is typically small for solids and liquids but much greater for gases. Increasing the pressure on an object decreases the volume of the object, increasing the temperature of a substance decreases its density by increasing its volume. In most materials, heating the bottom of a results in convection of the heat from the bottom to the top. This causes it to rise relative to more dense unheated material, the reciprocal of the density of a substance is occasionally called its specific volume, a term sometimes used in thermodynamics. Density is a property in that increasing the amount of a substance does not increase its density. Archimedes knew that the irregularly shaped wreath could be crushed into a cube whose volume could be calculated easily and compared with the mass, upon this discovery, he leapt from his bath and ran naked through the streets shouting, Eureka. As a result, the term eureka entered common parlance and is used today to indicate a moment of enlightenment, the story first appeared in written form in Vitruvius books of architecture, two centuries after it supposedly took place. Some scholars have doubted the accuracy of this tale, saying among other things that the method would have required precise measurements that would have been difficult to make at the time, from the equation for density, mass density has units of mass divided by volume. As there are units of mass and volume covering many different magnitudes there are a large number of units for mass density in use. The SI unit of kilogram per metre and the cgs unit of gram per cubic centimetre are probably the most commonly used units for density.1,000 kg/m3 equals 1 g/cm3. In industry, other larger or smaller units of mass and or volume are often more practical, see below for a list of some of the most common units of density
11.
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
12.
Aqueous solution
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An aqueous solution is a solution in which the solvent is water. It is usually shown in chemical equations by appending to the relevant chemical formula, for example, a solution of table salt, or sodium chloride, in water would be represented as Na+ + Cl−. The word aqueous means pertaining to, related to, similar to, as water is an excellent solvent and is also naturally abundant, it is a ubiquitous solvent in chemistry. Substances that are hydrophobic often do not dissolve well in water, an example of a hydrophilic substance is sodium chloride. Acids and bases are aqueous solutions, as part of their Arrhenius definitions, the ability of a substance to dissolve in water is determined by whether the substance can match or exceed the strong attractive forces that water molecules generate between themselves. If the substance lacks the ability to dissolve in water the molecules form a precipitate, reactions in aqueous solutions are usually metathesis reactions. Metathesis reactions are another term for double-displacement, that is, when a cation displaces to form a bond with the other anion. The cation bonded with the latter anion will dissociate and bond with the other anion, aqueous solutions that conduct electric current efficiently contain strong electrolytes, while ones that conduct poorly are considered to have weak electrolytes. Those strong electrolytes are substances that are ionized in water. Nonelectrolytes are substances that dissolve in water yet maintain their molecular integrity, examples include sugar, urea, glycerol, and methylsulfonylmethane. When writing the equations of reactions, it is essential to determine the precipitate. To determine the precipitate, one must consult a chart of solubility, soluble compounds are aqueous, while insoluble compounds are the precipitate. Remember that there may not always be a precipitate, when performing calculations regarding the reacting of one or more aqueous solutions, in general one must know the concentration, or molarity, of the aqueous solutions. Solution concentration is given in terms of the form of the prior to it dissolving. Metal ions in aqueous solution Solubility Dissociation Acid-base reaction theories Properties of water Zumdahl S.1997, 4th ed. Boston, Houghton Mifflin Company
13.
Solubility
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Solubility is the property of a solid, liquid, or gaseous chemical substance called solute to dissolve in a solid, liquid, or gaseous solvent. The solubility of a substance depends on the physical and chemical properties of the solute and solvent as well as on temperature, pressure. The solubility of a substance is a different property from the rate of solution. Most often, the solvent is a liquid, which can be a substance or a mixture. One may also speak of solid solution, but rarely of solution in a gas, the extent of solubility ranges widely, from infinitely soluble such as ethanol in water, to poorly soluble, such as silver chloride in water. The term insoluble is often applied to poorly or very poorly soluble compounds, a common threshold to describe something as insoluble is less than 0.1 g per 100 mL of solvent. Under certain conditions, the solubility can be exceeded to give a so-called supersaturated solution. Metastability of crystals can also lead to apparent differences in the amount of a chemical that dissolves depending on its form or particle size. A supersaturated solution generally crystallises when seed crystals are introduced and rapid equilibration occurs, phenylsalicylate is one such simple observable substance when fully melted and then cooled below its fusion point. Solubility is not to be confused with the ability to dissolve a substance, for example, zinc dissolves in hydrochloric acid as a result of a chemical reaction releasing hydrogen gas in a displacement reaction. The zinc ions are soluble in the acid, the smaller a particle is, the faster it dissolves although there are many factors to add to this generalization. Crucially solubility applies to all areas of chemistry, geochemistry, inorganic, physical, organic, in all cases it will depend on the physical conditions and the enthalpy and entropy directly relating to the solvents and solutes concerned. By far the most common solvent in chemistry is water which is a solvent for most ionic compounds as well as a range of organic substances. This is a factor in acidity/alkalinity and much environmental and geochemical work. According to the IUPAC definition, solubility is the composition of a saturated solution expressed as a proportion of a designated solute in a designated solvent. Solubility may be stated in units of concentration such as molarity, molality, mole fraction, mole ratio, mass per volume. Solubility occurs under dynamic equilibrium, which means that solubility results from the simultaneous and opposing processes of dissolution, the solubility equilibrium occurs when the two processes proceed at a constant rate. The term solubility is used in some fields where the solute is altered by solvolysis
14.
Acid dissociation constant
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An acid dissociation constant, Ka, is a quantitative measure of the strength of an acid in solution. It is the constant for a chemical reaction known as dissociation in the context of acid–base reactions. In the example shown in the figure, HA represents acetic acid, and A− represents the acetate ion, the chemical species HA, A− and H3O+ are said to be in equilibrium when their concentrations do not change with the passing of time. The definition can then be more simply H A ⇌ A − + H +, K a = This is the definition in common usage. A weak acid has a pKa value in the approximate range −2 to 12 in water, pKa values for strong acids can, however, be estimated by theoretical means. The definition can be extended to non-aqueous solvents, such as acetonitrile and dimethylsulfoxide. Denoting a solvent molecule by S H A + S ⇌ A − + S H +, K a = When the concentration of solvent molecules can be taken to be constant, K a =, as before. The value of pKa also depends on structure of the acid in many ways. For example, Pauling proposed two rules, one for successive pKa of polyprotic acids, and one to estimate the pKa of oxyacids based on the number of =O and −OH groups. Other structural factors that influence the magnitude of the dissociation constant include inductive effects, mesomeric effects. Hammett type equations have frequently applied to the estimation of pKa. The quantitative behaviour of acids and bases in solution can be only if their pKa values are known. These calculations find application in different areas of chemistry, biology, medicine. Acid dissociation constants are essential in aquatic chemistry and chemical oceanography. In living organisms, acid–base homeostasis and enzyme kinetics are dependent on the pKa values of the acids and bases present in the cell. According to Arrheniuss original definition, an acid is a substance that dissociates in solution, releasing the hydrogen ion H+. The equilibrium constant for this reaction is known as a dissociation constant. Brønsted and Lowry generalised this further to an exchange reaction
15.
Tannin
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A tannin is an astringent, polyphenolic biomolecule that binds to and precipitates proteins and various other organic compounds including amino acids and alkaloids. The term tannin refers to the use of wood tannins from oak in tanning hides into leather, hence the words tan. The tannin compounds are distributed in many species of plants, where they play a role in protection from predation, and perhaps also as pesticides. The astringency from the tannins is what causes the dry and puckery feeling in the following the consumption of unripened fruit or red wine or tea. Likewise, the destruction or modification of tannins with time plays an important role when determining harvesting times, Tannins have molecular weights ranging from 500 to over 3,000 and up to 20,000. There are three classes of tannins, Shown below are the base unit or monomer of the tannin. Particularly in the flavone-derived tannins, the base shown must be heavily hydroxylated and polymerized in order to give the high molecular weight polyphenol motif that characterizes tannins, typically, tannin molecules require at least 12 hydroxyl groups and at least five phenyl groups to function as protein binders. Oligostilbenoids are oligomeric forms of stilbenoids and constitute a class of tannins, pseudo tannins are low molecular weight compounds associated with other compounds. They do not change color during the Goldbeaters skin test, unlike hydrolysable and condensed tannins, some examples of pseudo tannins and their sources are, Ellagic acid, gallic acid, and pyrogallic acid were first discovered by chemist Henri Braconnot in 1831. Julius Löwe was the first person to synthesize ellagic acid by heating gallic acid with arsenic acid or silver oxide, maximilian Nierenstein studied natural phenols and tannins found in different plant species. Working with Arthur George Perkin, he prepared ellagic acid from algarobilla and he suggested its formation from galloyl-glycine by Penicillium in 1915. Tannase is an enzyme that Nierenstein used to produce acid from gallotannins. He proved the presence of catechin in cocoa beans in 1931 and he showed in 1945 that luteic acid, a molecule present in the myrobalanitannin, a tannin found in the fruit of Terminalia chebula, is an intermediary compound in the synthesis of ellagic acid. At these times, molecule formulas were determined through combustion analysis, the discovery in 1943 by Martin and Synge of paper chromatography provided for the first time the means of surveying the phenolic constituents of plants and for their separation and identification. There was an explosion of activity in this field after 1945, none more so than that of Edgar Charles Bate-Smith and it is referred to as the White–Bate-Smith–Swain–Haslam definition. Tannins are distributed in species throughout the plant kingdom and they are commonly found in both gymnosperms as well as angiosperms. Mole studied the distribution of tannin in 180 families of dicotyledons and 44 families of monocotyledons, most families of dicot contain tannin-free species. To the family of the oak, Fagaceae, 73% of the species tested contain tannin, for those of acacias, Mimosaceae, only 39% of the species tested contain tannin, among Solanaceae rate drops to 6% and 4% for the Asteraceae
16.
Polyphenol
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Polyphenols are a structural class of mainly natural, but also synthetic or semisynthetic, organic chemicals characterized by the presence of large multiples of phenol structural units. The number and characteristics of these phenol structures underlie the unique physical, chemical, examples include tannic acid and ellagitannin. The historically important chemical class of tannins is a subset of the polyphenols, the term polyphenol appears to have been in use since 1894. g. Phenyl esters, methyl phenyl ethers and O-phenyl glycosides and this definition departs from the WBSSH definition in terms of physicochemical behavior, with its lack of reference to solubility, precipitation, and complexation phenomena. The raspberry ellagitannin, on the hand, with its 14 gallic acid moieties. Individual polyphenols engage in related to both their core phenolic structures, their linkages, and types of glycosides they form. In addition, as noted above, a feature of polyphenols was their ability to form particular. As opposed to smaller phenols, polyphenols are often larger molecules deposited in cell vacuoles, hence, many larger polyphenols are biosynthesized in-situ from smaller polyphenols to nonhydrolyzable tannins and remain undiscovered in the plant matrix. Most polyphenols contain repeating phenolic moieties of pyrocatechol, resorcinol, pyrogallol, proanthocyanidins are mostly polymeric units of catechin and epicatechin. The phenolic substructures arise from various biosynthetic pathways, especially phenylpropanoid and polyketide branches aimed at plant, in these, diverse biosynthetic steps abound, the seven-atom ring appearing in theaflavin structure above is an example of a carbocycle that is of a nonbenzenoid aromatic tropolone type. Because of the preponderance of saccharide-derived core structures, as well as spiro- and other structure types, the total synthesis of a fully unmasked polyphenol, that of the ellagitannin tellimagrandin I, was a diastereoselective sequence reported in 1994 by Feldman, Ensel and Minard. Khanbabaee and Grosser accomplished a relatively efficient total synthesis of pedunculagin in 2003, work proceeded with focus on enantioselective total syntheses, e. g. A biomimetic synthesis, and the first formal total synthesis 5-O-Desgalloyl-epi-punicacortein A, the novel strategies and methods referred to in these recent examples helped to open the field of polyphenol chemical synthesis to an unprecedented degree. They are reactive species toward oxidation, ABTS may be used to characterise polyphenol oxidation products. Polyphenols also characteristically possess a significant binding affinity for proteins, which can lead to the formation of soluble and insoluble protein-polyphenol complexes, some polyphenols are traditionally used as dyes. For instance, in the Indian subcontinent, the peel, high in tannins and other polyphenols. The aims are generally to use of plant residues from grape. Cashew nut shell liquid is an important phenolic raw material containing mostly cardol, cardanol, pyrogallol and pyrocatechin are among the oldest photographic developers
17.
Acid
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An acid is a molecule or ion capable of donating a hydron, or, alternatively, capable of forming a covalent bond with an electron pair. The first category of acids is the donors or Brønsted acids. In the special case of solutions, proton donors form the hydronium ion H3O+ and are known as Arrhenius acids. Brønsted and Lowry generalized the Arrhenius theory to include non-aqueous solvents, acids form aqueous solutions with a sour taste, can turn blue litmus red, and react with bases and certain metals to form salts. The word acid is derived from the Latin acidus/acēre meaning sour, an aqueous solution of an acid has a pH less than 7 and is colloquially also referred to as acid, while the strict definition refers only to the solute. A lower pH means a higher acidity, and thus a higher concentration of hydrogen ions in the solution. Chemicals or substances having the property of an acid are said to be acidic, common aqueous acids include hydrochloric acid, acetic acid, sulfuric acid, and citric acid. As these examples show, acids can be solutions or pure substances, strong acids and some concentrated weak acids are corrosive, but there are exceptions such as carboranes and boric acid. The second category of acids are Lewis acids, which form a covalent bond with an electron pair, however, hydrogen chloride, acetic acid, and most other Brønsted-Lowry acids cannot form a covalent bond with an electron pair and are therefore not Lewis acids. Conversely, many Lewis acids are not Arrhenius or Brønsted-Lowry acids, in modern terminology, an acid is implicitly a Brønsted acid and not a Lewis acid, since chemists almost always refer to a Lewis acid explicitly as a Lewis acid. Modern definitions are concerned with the chemical reactions common to all acids. Most acids encountered in life are aqueous solutions, or can be dissolved in water, so the Arrhenius. The Brønsted-Lowry definition is the most widely used definition, unless otherwise specified, hydronium ions are acids according to all three definitions. Interestingly, although alcohols and amines can be Brønsted-Lowry acids, they can function as Lewis bases due to the lone pairs of electrons on their oxygen and nitrogen atoms. The Swedish chemist Svante Arrhenius attributed the properties of acidity to hydrogen ions or protons in 1884, an Arrhenius acid is a substance that, when added to water, increases the concentration of H+ ions in the water. Thus, an Arrhenius acid can also be described as a substance that increases the concentration of ions when added to water. Examples include molecular substances such as HCl and acetic acid, an Arrhenius base, on the other hand, is a substance which increases the concentration of hydroxide ions when dissolved in water. Thus, an Arrhenius acid could also be said to be one that decreases hydroxide concentration, in an acidic solution, the concentration of hydronium ions is greater than 10−7 moles per liter
18.
Phenol
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Phenol, also known as carbolic acid, is an aromatic organic compound with the molecular formula C6H5OH. It is a crystalline solid that is volatile. The molecule consists of a phenyl group bonded to a hydroxyl group and it is mildly acidic and requires careful handling due to its propensity to cause chemical burns. Phenol was first extracted from tar, but today is produced on a large scale from petroleum. It is an important industrial commodity as a precursor to many materials and it is primarily used to synthesize plastics and related materials. Phenol and its derivatives are essential for production of polycarbonates, epoxies, Bakelite, nylon, detergents, herbicides such as phenoxy herbicides. Phenol is appreciably soluble in water, with about 84.2 g dissolving in 1000 mL, homogeneous mixtures of phenol and water at phenol to water mass ratios of ~2.6 and higher are possible. The sodium salt of phenol, sodium phenoxide, is far more water-soluble and it reacts completely with aqueous NaOH to lose H+, whereas most alcohols react only partially. One explanation for the increased acidity over alcohols is resonance stabilization of the anion by the aromatic ring. In this way, the charge on oxygen is delocalized on to the ortho. In another explanation, increased acidity is the result of orbital overlap between the lone pairs and the aromatic system. The pKa of the enol of acetone is 10.9, the acidities of phenol and acetone enol diverge in the gas phase owing to the effects of solvation. About 1⁄3 of the acidity of phenol is attributable to inductive effects. Phenolate esters are more stable toward hydrolysis than acid anhydrides and acyl halides but are sufficiently reactive under mild conditions to facilitate the formation of amide bonds, Phenol exhibits keto-enol tautomerism with its unstable keto tautomer cyclohexadienone, but only a tiny fraction of phenol exists as the keto form. The equilibrium constant for enolisation is approximately 10−13, meaning only one in every ten trillion molecules is in the keto form at any moment. The small amount of stabilisation gained by exchanging a C=C bond for a C=O bond is more than offset by the large destabilisation resulting from the loss of aromaticity, Phenol therefore exists essentially entirely in the enol form. Phenoxides are enolates stabilised by aromaticity, under normal circumstances, phenoxide is more reactive at the oxygen position, but the oxygen position is a hard nucleophile whereas the alpha-carbon positions tend to be soft. Phenol is highly reactive toward electrophilic aromatic substitution as the oxygen atoms pi electrons donate electron density into the ring, by this general approach, many groups can be appended to the ring, via halogenation, acylation, sulfonation, and other processes
19.
Tara spinosa
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Caesalpinia spinosa Kuntze, commonly known as tara, is a small leguminous tree or thorny shrub native to Peru. C. spinosa is cultivated as a source of tannins based on a galloylated quinic acid structure and this chemical structure has been confirmed also by LC-MS. It is also grown as a plant because of its large colorful flowers. C. tara, C. tinctoria HBK, Coulteria tinctoria HBK, Tara spinosa, common names, Spiny holdback, tara, taya, algarroba tanino. C. spinosa is in the Fabaceae family, depending on the system, the Caesalpinioideae subfamily. C. spinosa typically grows 2–5 m tall, its bark is gray with scattered prickles. Leaves are alternate, evergreen, lacking stipules, bipinnate, and lacking petiolar, leaves consist of three to 10 pairs of primary leaflets under 8 cm in length, and five to seven pairs of subsessile elliptic secondary leaflets, each about 1. 5–4 cm long. Inflorescences are 15–20 cm long racemes, many flowered and covered in tiny hairs. Flowers are yellow to orange with 6- to 7-mm petals, the lowest sepal is boat-shaped with many long marginal teeth, stamens are yellow, irregular in length and barely protruding. The fruit is a flat, oblong indehiscent pod, about 6–12 cm long and 2.5 cm wide, containing four to seven round black seeds, which redden when mature. C. spinosa is native to Peru and can be found growing throughout northern, western and southern South America and it has been introduced in drier parts of Asia, the Middle East and Africa and has become naturalized in California. C. spinosa grows in the nearly rainless lomas or fog oases of the Peruvian coastal desert. Generally resistant to most pathogens and pests, it will grow between 0 and 3,000 meters above sea level, tolerates dry climates and poor soils including those high in sand and rocks. To propagate, seeds must be scarified, and young plants should be transplanted to the field at 40 cm in height, mature pods are usually harvested by hand and typically sun dried before processing. If well irrigated, trees can continue to produce for another 80 years, C. spinosa pods are an excellent source of environmentally friendly tannins most commonly used in the manufacture of automotive and furniture leathers. This growing industry is developing around their production in Peru, some producers have their own plantations to guarantee constant quality. Tara tannin derivatives are being proposed as antifouling against marine organisms that can grow on ship hulls and those tannins are of the hydrolysable type. Gallic acid is the constituent of tara tannins and can be easily isolated by alkaline hydrolysis of the plant extract
20.
Rhus chinensis
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Rhus chinensis, the Chinese sumac or nutgall tree, is a plant species in the genus Rhus. The species is used to produce galls, called Chinese gall, Galla Chinensis or Wu Bei Zi in Chinese, which are rich in gallotannins, the infestation by Chinese sumac aphids can lead to a gall which is valued as a commercial product. Chinese galls are used in Chinese medicine to treat coughs, diarrhea, night sweats, dysentery and to stop intestinal, Rhus chinensis compounds possess strong antiviral, antibacterial, anticancer, hepatoprotective, antidiarrheal and antioxidant activities. The gall of Rhus chinensis, Galla chinensi, has long considered to possess many medicinal properties. Gallic acid, isolated from Rhus chinensis, induces apoptosis in human monocytic lymphoma cell line U937, the gall of Rhus chinensis inhibits alpha-glucosidase activity. Rhus chinensis on www. ars-grin. gov Plants for a Future PFAF. org
21.
Quercus infectoria
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Quercus infectoria is a species of oak, bearing galls that have been traditionally used for centuries in Asia medicinally. Quercus infectoria or locally known as Manjakani in Malaysia is a tree native of Greece and Asia Minor. The stems are crooked, shrubby looking with smooth and bright-green leaves borne on petioles of 1 to 1.5 inches long. The leaves are bluntly mucronate, rounded, smooth, unequal at the base, meanwhile, Quercus infectoria galls are corrugated and can be used as a thickener in stews or mixed with cereals for making bread. The galls arise on young branches of tree as a result of attacks by gall wasps. Also known as Majuphal in Indian traditional medicine, manjakani has been used as powder and in the treatment of toothache. The so-called Aleppo tannin is Tannic acid gained from Aleppo oak galls, nowadays, gallnut extracts are also widely used in pharmaceuticals, food and feed additives, dyes, inks, and metallurgy. The main constituents found in the galls of Quercus infectoria are tannin and small amount of free gallic acid, the nutgalls have been pharmacologically documented on their antiamoebic, anticariogenic and anti-inflammatory activities, to treat skin infections and gastrointestinal disorders. The galls from Quercus infectoria contain the highest naturally occurring level of tannin, 50–70%, syringic acid, β-sitosterol, amentoflavone, hexamethyl ether, isocryptomerin, methyl betulate, methyl oleanate and hexagalloyl glucose. They also contain 2-4% each of gallic and ellagic acid that are polymerized to make tannins, Tannins have been used for hundreds of years for medical purposes and are currently indispensable in dermatology and have been used for tanning of leather. Tannins comprise a group of natural products widely distributed in the plant kingdom. They have a great diversity, but are usually divided into two basic groups, the hydrolyzable type and the condensed type. Hydrolyzable tannins include the commonly occurring gallic and ellagic acid contained in the nutgalls, the gallic and ellagic acid hydrolyzable tannins react with proteins to produce typical tanning effects, medicinally, this is important to treat inflamed or ulcerated tissues. They also contribute to most of the astringent property of manjakani and are great for vaginal tightening. Although both types of tannin have been used to treat diseases in medicine, the hydrolyzable tannins have long been considered official medicinal agents in Europe. They have been included in many pharmacopoeias, in the editions in particular. These were recommended for treatment of inflammation and ulceration, including topical application for skin diseases and internal use for intestinal ulceration, now, the condensed tannins also have important medicinal roles, such as stable and potent antioxidants. In China, tannin-containing substances, such as galls, pomegranate rinds, the potential of aqueous and acetone extracts of galls of Quercus infectoria as antibacterial agents Gallnuts and the Uses of Tannins in Chinese Medicine
22.
Rhus coriaria
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Rhus coriaria, commonly called Sicilian sumac, tanners sumach, or elm-leaved sumach, is a deciduous shrub to small tree in the Anacardiaceae or Cashew family, native to southern Europe. The dried fruits are used as a spice, particularly in combination with other spices in the mixture called Zaatar, the plant will grow in any type of soil that is deep and well-drained. Caution should be used about consuming sumac, the fruit has a sour taste, dried and crushed, it is a popular spice in the Middle East. Immature fruits and seeds are also eaten, the leaves and the bark were traditionally used in tanning and contain tannic acid. Dyes of various colours, red, yellow, black, and brown and it has been postulated that the sap and the fruit contain toxins that can cause severe irritation in people who are sensitive to these compounds. Because of its relationship to other urushiol-containing species of the genus Rhus. However, cases involving pure Rhus coriaria have not been documented in medical literature
23.
Chestnut
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The chestnut group is a genus of eight or nine species of deciduous trees and shrubs in the beech family Fagaceae, native to temperate regions of the Northern Hemisphere. The name also refers to the edible nuts they produce, Chestnuts belong to the family Fagaceae, which also includes oaks and beeches. Unrelated but externally similar species of horse chestnut are abundant around Europe, other trees commonly mistaken for chestnut trees are the chestnut oak and the American beech, both of which are also in Fagaceae. The name chestnut is derived from an earlier English term chesten nut, the name Castanea is probably derived from the old name for the sweet chestnut, either in Latin or in Ancient Greek. Another possible source of the name is the town of Kastania in Thessaly, Greece, more probable, in the Mediterranean climate zone, chestnut trees are rarer in Greece because the chalky soil is not conducive to the trees growth. Kastania is located on one of the relatively few sedimentary or siliceous outcrops and they grow so abundantly there, their presence would have determined the places name. Still others take the name as coming from the Greek name of Sardis glans – Sardis being the capital of Lydia, Asia Minor, the name is cited twice in the King James Version of the Bible. In one instance, Jacob puts peeled twigs in the troughs to promote healthy offspring of his livestock. Although it may indicate another tree, it indicates the fruit was a staple food in the early 17th century. These synonyms are or have been in use, Fagus castanea, Sardian nut, Jupiters nut, husked nut, Chestnut trees are of moderate growth rate to fast-growing for American and European species. Their mature heights vary from the smallest species of chinkapins, often shrubby, to the giant of past American forests, C. dentata that could reach 60 m. Between these extremes are found the Japanese chestnut at 10 m average, followed by the Chinese chestnut at about 15 m, when standing on their own, they spread on the sides and develop broad, rounded, dense crowns at maturity. The two latters foliage has striking yellow autumn colouring and its bark is smooth when young, of a vinous maroon or red-brown colour for the American chestnut, grey for the European chestnut. The leaves are simple, ovate or lanceolate, 10–30 cm long and 4–10 cm wide, with sharply pointed, the flowers follow the leaves, appearing in late spring or early summer or into July. They are arranged in long catkins of two kinds, with both kinds being borne on every tree, some catkins are made of only male flowers, which mature first. Each flower has eight stamens, or 10 to 12 for C. mollissima, the ripe pollen carries a heavy, sweet odour that some people find too sweet or unpleasant. Other catkins have these pollen-bearing flowers, but also carry near the twig from which these spring, two or three flowers together form a four-lobed prickly calybium, which ultimately grows completely together to make the brown hull, or husk, covering the fruits. Chestnut flowers are not self-compatible, so two trees are required for pollination, all Castanea species readily hybridize with each other
24.
Oak
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An oak is a tree or shrub in the genus Quercus of the beech family, Fagaceae. There are approximately 600 extant species of oaks, the common name oak also appears in the names of species in related genera, notably Lithocarpus, as well as in those of unrelated species such as Grevillea robusta and the Casuarinaceae. North America contains the largest number of oak species, with approximately 90 occurring in the United States, the second greatest center of oak diversity is China, which contains approximately 100 species. Oaks have spirally arranged leaves, with lobate margins in many species, also, the acorns contain tannic acid, as do the leaves, which helps to guard from fungi and insects. Many deciduous species are marcescent, not dropping dead leaves until spring, in spring, a single oak tree produces both male flowers and small female flowers. The fruit is a nut called an acorn, borne in a structure known as a cupule, each acorn contains one seed and takes 6–18 months to mature. The live oaks are distinguished for being evergreen, but are not actually a distinct group, the oak tree is a flowering plant. Oaks may be divided into two genera and a number of sections, The genus Quercus is divided into the following sections, Quercus, the white oaks of Europe, Asia and North America. Styles are short, acorns mature in 6 months and taste sweet or slightly bitter, the leaves mostly lack a bristle on their lobe tips, which are usually rounded. The type species is Quercus robur, Mesobalanus, Hungarian oak and its relatives of Europe and Asia. Styles long, acorns mature in about 6 months and taste bitter, the section Mesobalanus is closely related to section Quercus and sometimes included in it. Cerris, the Turkey oak and its relatives of Europe and Asia, styles long, acorn mature in 18 months and taste very bitter. The inside of the shell is hairless. Its leaves typically have sharp tips, with bristles at the lobe tip. Protobalanus, the live oak and its relatives, in southwest United States. Styles short, acorns mature in 18 months and taste very bitter, the inside of the acorn shell appears woolly. Leaves typically have sharp tips, with bristles at the lobe tip. Lobatae, the red oaks of North America, Central America, styles long, acorns mature in 18 months and taste very bitter
25.
Amorphous solid
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In condensed matter physics and materials science, an amorphous or non-crystalline solid is a solid that lacks the long-range order that is characteristic of a crystal. In some older books, the term has been used synonymously with glass, nowadays, glassy solid or amorphous solid is considered to be the overarching concept, and glass the more special case, A glass is an amorphous solid that exhibits a glass transition. Other types of solids include gels, thin films. Amorphous materials have a structure made of interconnected structural blocks. Even amorphous materials have some shortrange order at the length scale due to the nature of chemical bonding. Furthermore, in small crystals a large fraction of the atoms are the crystal, relaxation of the surface and interfacial effects distort the atomic positions. Amorphous phases are important constituents of thin films, which are layers of a few nm to some tens of µm thickness deposited upon a substrate. For higher values, the diffusion of deposited atomic species would allow for the formation of crystallites with long range atomic order. Regarding their applications, amorphous metallic layers played an important role in the discussion of a suspected superconductivity in amorphous metals, today, optical coatings made from TiO2, SiO2, Ta2O5 etc. and combinations of them in most cases consist of amorphous phases of these compounds. Much research is carried out into thin films as a gas separating membrane layer. Also, hydrogenated amorphous silicon, a-Si, H in short, is of significance for thin film solar cells. In case of a-Si, H the missing long-range order between silicon atoms is partly induced by the presence by hydrogen in the percent range, the occurrence of amorphous phases turned out as a phenomenon of particular interest for studying thin film growth. Remarkably, the growth of polycrystalline films is used and preceded by an initial amorphous layer. The most investigated example is represented by thin multicrystalline silicon films, an initial amorphous layer was observed in many studies. The phenomenon has been interpreted in the framework of Ostwalds rule of stages that predicts the formation of phases to proceed with increasing condensation time towards increasing stability. Experimental studies of the phenomenon require a clearly defined state of the substrate surface, the Physics of Structurally Disordered Matter, An Introduction. Amorphous Solids and the Liquid State
26.
Gram
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The gram is a metric system unit of mass. Originally defined as the weight of a volume of pure water equal to the cube of the hundredth part of a metre. The only unit symbol for gram that is recognised by the International System of Units is g following the numeric value with a space, the SI does not support the use of abbreviations such as gr, gm or Gm. The word gramme was adopted by the French National Convention in its 1795 decree revising the system as replacing the gravet introduced in 1793. Its definition remained that of the weight of a centimetre of water. French gramme was taken from the Late Latin term gramma and this word, ultimately from Greek γράμμα letter had adopted a specialised meaning in Late Antiquity of one twenty-fourth part of an ounce, corresponding to about 1.14 grams. This use of the term is found in the carmen de ponderibus et mensuris composed around 400 AD, the gram was the fundamental unit of mass in the 19th-century centimetre–gram–second system of units. The gram is today the most widely used unit of measurement for non-liquid ingredients in cooking and grocery shopping worldwide. 1 gram =15.4323583529 grains 1 grain =0.06479891 grams 1 avoirdupois ounce =28.349523125 grams 1 troy ounce =31.1034768 grams 100 grams =3.527396195 ounces 1 gram =5 carats 1 gram =8. 1 gram is roughly equal to 1 small paper clip or pen cap, the Japanese 1 yen coin has a mass of one gram. Conversion of units Duella Gold gram Orders of magnitude Gram at Encyclopædia Britannica
27.
Litre
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The litre or liter is an SI accepted metric system unit of volume equal to 1 cubic decimetre,1,000 cubic centimetres or 1/1,000 cubic metre. A cubic decimetre occupies a volume of 10×10×10 centimetres and is equal to one-thousandth of a cubic metre. The original French metric system used the litre as a base unit. The word litre is derived from an older French unit, the litron, whose name came from Greek — where it was a unit of weight, not volume — via Latin, and which equalled approximately 0.831 litres. The litre was also used in subsequent versions of the metric system and is accepted for use with the SI. The spelling used by the International Bureau of Weights and Measures is litre, the less common spelling of liter is more predominantly used in American English. One litre of water has a mass of almost exactly one kilogram. Subsequent redefinitions of the metre and kilogram mean that this relationship is no longer exact, a litre is defined as a special name for a cubic decimetre or 10 centimetres ×10 centimetres ×10 centimetres. Hence 1 L ≡0.001 m3 ≡1000 cm3, from 1901 to 1964, the litre was defined as the volume of one kilogram of pure water at maximum density and standard pressure. The kilogram was in turn specified as the mass of a platinum/iridium cylinder held at Sèvres in France and was intended to be of the mass as the 1 litre of water referred to above. It was subsequently discovered that the cylinder was around 28 parts per million too large and thus, during this time, additionally, the mass-volume relationship of water depends on temperature, pressure, purity and isotopic uniformity. In 1964, the definition relating the litre to mass was abandoned in favour of the current one, although the litre is not an official SI unit, it is accepted by the CGPM for use with the SI. CGPM defines the litre and its acceptable symbols, a litre is equal in volume to the millistere, an obsolete non-SI metric unit customarily used for dry measure. The litre is often used in some calculated measurements, such as density. One litre of water has a mass of almost exactly one kilogram when measured at its maximal density, similarly,1 millilitre of water has a mass of about 1 g,1,000 litres of water has a mass of about 1,000 kg. It is now known that density of water depends on the isotopic ratios of the oxygen and hydrogen atoms in a particular sample. The litre, though not an official SI unit, may be used with SI prefixes, the most commonly used derived unit is the millilitre, defined as one-thousandth of a litre, and also often referred to by the SI derived unit name cubic centimetre. It is a commonly used measure, especially in medicine and cooking, Other units may be found in the table below, where the more often used terms are in bold
28.
Mole (unit)
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The mole is the unit of measurement in the International System of Units for amount of substance. This number is expressed by the Avogadro constant, which has a value of 6. 022140857×1023 mol−1, the mole is one of the base units of the SI, and has the unit symbol mol. The mole is used in chemistry as a convenient way to express amounts of reactants and products of chemical reactions. For example, the chemical equation 2 H2 + O2 →2 H2O implies that 2 moles of dihydrogen and 1 mole of dioxygen react to form 2 moles of water. The mole may also be used to express the number of atoms, ions, the concentration of a solution is commonly expressed by its molarity, defined as the number of moles of the dissolved substance per litre of solution. For example, the relative molecular mass of natural water is about 18.015, therefore. The term gram-molecule was formerly used for essentially the same concept, the term gram-atom has been used for a related but distinct concept, namely a quantity of a substance that contains Avogadros number of atoms, whether isolated or combined in molecules. Thus, for example,1 mole of MgBr2 is 1 gram-molecule of MgBr2 but 3 gram-atoms of MgBr2, in honor of the unit, some chemists celebrate October 23, which is a reference to the 1023 scale of the Avogadro constant, as Mole Day. Some also do the same for February 6 and June 2, thus, by definition, one mole of pure 12C has a mass of exactly 12 g. It also follows from the definition that X moles of any substance will contain the number of molecules as X moles of any other substance. The mass per mole of a substance is called its molar mass, the number of elementary entities in a sample of a substance is technically called its amount. Therefore, the mole is a convenient unit for that physical quantity, one can determine the chemical amount of a known substance, in moles, by dividing the samples mass by the substances molar mass. Other methods include the use of the volume or the measurement of electric charge. The mass of one mole of a substance depends not only on its molecular formula, since the definition of the gram is not mathematically tied to that of the atomic mass unit, the number NA of molecules in a mole must be determined experimentally. The value adopted by CODATA in 2010 is NA =6. 02214129×1023 ±0. 00000027×1023, in 2011 the measurement was refined to 6. 02214078×1023 ±0. 00000018×1023. The number of moles of a sample is the sample mass divided by the mass of the material. The history of the mole is intertwined with that of mass, atomic mass unit, Avogadros number. The first table of atomic mass was published by John Dalton in 1805
29.
Tanbark
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Tanbark is the bark of certain species of tree. It is traditionally used for tanning hides into leather, the words tannin, tanning, tan, and tawny are derived from the Medieval Latin tannare, to convert into leather. Bark mills are horse- or oxen-driven or water powered edge mills and were used in times to shred the tanbark to derive tannins for the leather industry. A barker was a person who stripped bark from trees to supply bark mills, in Europe, oak is a common source of tanbark. Quercitannic acid is the constituent found in oak barks. The bark is taken from branches and twigs in oak coppices and can be up to 4 mm thick, it is grayish-brown on the outside. In some areas of the United States, such as northern California, tanbark is often called mulch, in these areas, the word mulch may refer to peat moss or to very fine tanbark. In California, Lithocarpus densiflorus was used, in America, condensed tannins are also present in the bark of blackjack oak. In New York, on the slopes of Mount Tremper, hemlock bark was a source of tanbark during the 19th century. Around the Mediterranean Sea, sumach leaves and bark are used, in Africa and Australia, acacia bark is used by tanners
30.
Tannic acid
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Tannic acid is a specific form of tannin, a type of polyphenol. Its weak acidity is due to the numerous groups in the structure. Commercial tannic acid is extracted from any of the following plant part, Tara pods. Sometimes extracts from chestnut or oak wood are also described as tannic acid and it is a yellow to light brown amorphous powder,2850 grams dissolves in one litre of water. While tannic acid is a type of tannin, the two terms are sometimes used interchangeably. The long-standing misuse of the terms, and its inclusion in scholarly articles has compounded the confusion and this is particularly widespread in relation to green tea and black tea, both of which contain tannin but not tannic acid. Tannic acid is not a standard for any type of tannin analysis because of its poorly defined composition. Quercitannic acid is one of the two forms of acid found in oak bark and leaves. The other form is called gallotannic acid and is found in oak galls, the quercitannic acid molecule is also present in quercitron, a yellow dye obtained from the bark of the Eastern black oak, a forest tree indigenous in North America. It is described as a yellowish brown amorphous substance, in 1838, Jöns Jacob Berzelius wrote that quercitannate is used to dissolve morphine. In 1865 in the volume of A dictionary of chemistry, Henry Watts wrote. It differs however from the latter in not being convertible into gallic acid and it is precipitated by sulfuric acid in red flocks. According to Rochleder, the acid of black tea is the same as that of oak-bark. In 1880, Etti gave for it the molecular formula C17H16O9 and he described it as an unstable substance, having a tendency to give off water to form anhydrides, one of which is called oak-red. For him, it was not a glycoside, in Allen’s Commercial Organic Analysis, published in 1912, the formula given was C19H16O10. Other authors gave other molecular formulas like C28H26O15, while another formula found is C28H24O11, according to Lowe, two forms of the principle exist – one soluble in water, of the formula C28H28O14, and the other scarcely soluble, C28H24O12. Both are changed by the loss of water into oak red, quercitannic acid was for a time a standard used to assess the phenolic content in spices, given as quercitannic acid equivalent. In an interesting note, the inventor Edward G. Acheson discovered that gallotannic acid greatly improved the plasticity of clay
31.
Gallic acid
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Gallic acid is a trihydroxybenzoic acid, a type of phenolic acid, found in gallnuts, sumac, witch hazel, tea leaves, oak bark, and other plants. The chemical formula of gallic acid is C6H23COOH and it is found both free and as part of hydrolyzable tannins. The gallic acid groups are bonded to form dimers such as ellagic acid. Hydrolyzable tannins break down on hydrolysis to give gallic acid and glucose or ellagic acid and glucose, known as gallotannins and ellagitannins, gallic acid forms intermolecular esters such as digallic and trigallic acids, and cyclic ether-esters. Gallic acid can also be used as a material in the synthesis of the psychedelic alkaloid mescaline. The name is derived from oak galls, which were used to prepare tannic acid. Despite the name, gallic acid does not contain gallium, salts and esters of gallic acid are termed gallates. Pliny the Elder describes his experiments with it and writes that it was used to produce dyes, galls from oak trees were crushed and mixed with water, producing tannic acid. Gallic acid was one of the used by Angelo Mai, among other early investigators of palimpsests, to clear the top layer of text off. Mai was the first to employ it, but did so with a heavy hand, gallic acid was first studied by the Swedish chemist Carl Wilhelm Scheele in 1786. Gallic acid is a component of some pyrotechnic whistle mixtures, gallic acid is formed from 3-dehydroshikimate by the action of the enzyme shikimate dehydrogenase to produce 3, 5-didehydroshikimate. This latter compound tautomerizes to form the redox equivalent gallic acid, gallate dioxygenase is an enzyme found in Pseudomonas putida that catalyses the reaction gallate + O2 → -4-oxobut-1-ene-1,2, 4-tricarboxylate. Gallate decarboxylase is another enzyme in the degradation of gallic acid, gallate 1-beta-glucosyltransferase is an enzyme that uses UDP-glucose and gallate, whereas its two products are UDP and 1-galloyl-beta-D-glucose. It is a carbonic anhydrase inhibitor. In basic research, gallic acid extracted from seeds has been shown to inhibit the formation of amyloid fibrils, one of the potential causes of Alzheimers disease. One study indicated that gallic acid has this effect on amyloid protein formation by modifying the properties of alpha-synuclein, gallic acid is classified as a mutagen and a teratogen. Gallic acid is found in a number of plants, such as the parasitic plant Cynomorium coccineum, the aquatic plant Myriophyllum spicatum. Gallic acid is found in various oak species, Caesalpinia mimosoides
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Pyrogallol
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Pyrogallol is an organic compound with the formula C6H33. It is a white solid although samples are typically brownish because of its sensitivity toward oxygen and it is one of three isomeric benzenetriols. It is produced in the manner it was first prepared by Scheele, presently gallic acid is obtained from tannin. Heating induces decarboxylation, Because tannin is expensive, many routes have been devised. An alternate preparation involves treating para-chlorophenoldisulphonic acid with potassium hydroxide, a variant on the route to phenols from sulfonic acids. The aquatic plant Myriophyllum spicatum produces pyrogallic acid, when in alkaline solution, it absorbs oxygen from the air, turning brown from a colourless solution. It can be used in this way to calculate the amount of oxygen in air, one can find its uses in hair dying, dying of suturing materials and for oxygen absorption in gas analysis. Pyrogallol was also used as an agent in black-and-white developers. In those days it had a reputation for erratic and unreliable behavior and it experienced a revival starting in the 1980s due largely to the efforts of experimenters Gordon Hutchings and John Wimberley. Hutchings spent over a decade working on formulas, eventually producing one he named PMK. From 1969 to 1977, Wimberley experimented with the Pyrogallol developing agent and he published his formula for WD2D in 1977 in Petersons Photographic. PMK and other modern pyro formulations are now used by many black-and-white photographers, the Film Developing Cookbook has examples. Pyrogallol use, e. g. in hair dye formulations, is declining because of concerns about its toxicity
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John Stenhouse
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John Stenhouse FRS FRSE FIC FCS was a Scottish chemist. In 1854, he invented one of the first practical respirators and he was a co-founder of the Chemical Society in 1841. John Stenhouse was born in Glasgow on 21 October 1809 and he was the eldest son of William Stenhouse, a calico-printer in Glasgow, and Elizabeth Currie, he was the only one of their children to survive beyond infancy. After graduating from the Glasgow Grammar School, he studied at Glasgow University from 1824 to 1828, during 1837-1839, he attended the chemical lectures at Glasgow University, whence he left to pursue chemistry research for two years under Justus Liebig at the University of Giessen in Germany. In 1841 he was a co-founder of the Chemical Society of London, in 1848 he was elected a Fellow of the Royal Society of London. He received his LL. D. degree from the University of Aberdeen in 1850, hitherto Stenhouse had been living on a fortune that had been left to him by his father, however, in 1850 the Glasgow Commercial Exchange Company failed and his inheritance was lost. He then sought a professorship at Owens College, now the University of Manchester, however, in February 1851 he was appointed Lecturer on Chemistry to the medical school at St Bartholomews Hospital in London. In 1857 Stenhouse suffered a stroke, which left him paralyzed and forced him to resign his position. He left England to convalesce with his mother in Nice until her death in February 1860 and he also recommenced his researches in chemistry, even though he could not perform experiments with his own hands. He hired assistants to do the work for him, from 1865 to 1870 he was an assayer to the Royal Mint. In 1871 he received the Royal Medal of the Royal Society for his chemical researches, in 1877 he became a Fellow of the Institute of Chemistry. He died a death on 31 December 1880, age 72, at his home in Pentonville. Among other patents which he took out was one for the manufacture of glue and another for the manufacture or preparation of materials for sizing or dressing yarns and textile fabrics
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Organic acid anhydride
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An organic acid anhydride is an acid anhydride that is an organic compound. An acid anhydride is a compound that has two acyl groups bonded to the oxygen atom. A common type of acid anhydride is a carboxylic anhydride, where the parent acid is a carboxylic acid. Symmetrical acid anhydrides of this type are named by replacing the word acid in the name of the parent carboxylic acid by the word anhydride, thus, 2O is called acetic anhydride. Mixed acid anhydrides, such as acetic anhydride, are known. One or both groups of an acid anhydride may also be derived from another type of organic acid. One of the groups of an acid anhydride can be derived from an inorganic acid such as phosphoric acid. The mixed anhydride 1, 3-bisphosphoglycerate is an intermediate in the formation of ATP via glycolysis, is the mixed anhydride between 3-phosphoglyceric acid and phosphoric acid, acidic oxides are often classified as acid anhydrides. Acid anhydrides are prepared in industry by diverse means, Acetic anhydride is mainly produced by the carbonylation of methyl acetate. Maleic anhydride is produced by the oxidation of benzene or butane, laboratory routes emphasize the dehydration of the corresponding acids. In reactions with protic substrates, the reactions afford equal amounts of the acylated product, acid anhydrides tend to be less electrophilic than acyl chlorides, and only one acyl group is transferred per molecule of acid anhydride, which leads to a lower atom efficiency. The low cost, however, of acetic anhydride makes it a choice for acetylation reactions. Illustrative acid anhydrides Acetic anhydride is an industrial chemical widely used for preparing acetate esters. Maleic anhydride is the precursor to various resins by copolymerization with styrene, maleic anhydride is a dienophile in the Diels-Alder reaction. Dianhydrides, molecules containing two acid anhydride functions, are used to synthesize polyimides and sometimes polyesters and polyamides, polyanhydrides are a class of polymers characterized by anhydride bonds that connect repeat units of the polymer backbone chain. Natural organic acid anhydrides are rare, because of the reactivity of the functional group, examples include cantharidin from species of blister beetle, including the Spanish fly, Lytta vesicatoria, and tautomycin, from the bacterium Streptomyces spiroverticillatus. Sulfur can replace oxygen, either in the group or in the bridge. In the former case, the name of the group is enclosed in parentheses to avoid ambiguity in the name
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Phlobaphene
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Phlobaphenes are reddish, alcohol-soluble and water-insoluble phenolic substances. They can be extracted from plants, or be the result from treatment of tannin extracts with mineral acids, the name phlobaphen come from the Greek roots φλoιὀς meaning bark and βαφή meaning dye. No biological activities have currently been reported for phlobaphenes, phlobaphenes from hawthorn fruits may have a specific action on the coronary circulation. They are converted into humins in soils, natural phlobaphenes are the common bark, pericarp, cob glume and seed coat pigments. They have not been found in flowers, unless the brown, in bark, phlobaphenes accumulate in the phellem layer of cork cambium, part of the suberin mixture. Many cinchona barks contain a particular tannin, cinchotannic acid, which by oxidation rapidly yields a dark-coloured phlobaphene called red cinchonic, cinchono-fulvic acid or cinchona red, cuscuta europaea L. the European dodder, is reported to contain 30,000 ppm in the root. Phlobaphenes can be extracted from the root of the common tormentil as tormentil red, phlobaphens can be found in the kola nut, chocolate liquor or in the red skins or testa of the peanut. They are also reported in the fruits of the genus Crataegus or can be extracted from hop flowers, the chief constituent of kino is kinotannic acid, of which it contains 70 to 80 per cent. It also contains red, a phlobaphene produced from kinotannic acid by oxidation. Phlobaphenes are not present in the model plant Arabidopsis thaliana but can be studied as the pigment responsible for the red color in some monocot cereals, including wheat, maize or sorghum. The maize P gene encodes a Myb homolog that recognizes the sequence CCT/AACC and it is a dark-colored resin-like substance made of water-insoluble, alcohol-soluble polymers. Phlobaphens can be formed under action of acids or heating of condensed tannins or of the fraction of tannins called phlobatannins, water containing soda can be used for the conversion of hop tannins into phlobaphens. When heated with hydrochloric acid, tannins in cocoa solids yield a glucose, ordinary or warm soluble quebracho is the natural extract obtained directly from the quebracho wood. This type of extract is rich in condensed tannins of natural high molecular weight and its use is therefore limited to small additions during sole leather tannage carried out in hot liquors to improve the yield and the water-proofness of the leather. The cold soluble extracts are obtained by subjecting the ordinary extract to a process which transforms the phlobaphenes into completely soluble tannins. The cold soluble extracts are the most universally known and used types. The main properties of these extracts are, a rapid penetration, a high tannin content. The rather low acid and medium salt content characterise them as mild tanning extracts, phlobaphenes formation can be minimized in using strong nucleophiles, such as phloroglucinol, m-phenylenediamine and urea, during pine tannins extraction
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Spice
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A spice is a seed, fruit, root, bark, or other plant substance primarily used for flavoring, coloring or preserving food. Spices are distinguished from herbs, which are the leaves, flowers, sometimes, spices may be ground into a powder for convenience. Spices are sometimes used in medicine, religious rituals, cosmetics or perfume production, the spice trade developed throughout South Asia and Middle East by at least 2000 BCE with cinnamon and black pepper, and in East Asia with herbs and pepper. The Egyptians used herbs for mummification and their demand for exotic spices and herbs helped stimulate world trade. The word spice comes from the Old French word espice, which became epice, and which came from the Latin root spec, by 1000 BCE, medical systems based upon herbs could be found in China, Korea, and India. Early uses were connected with magic, medicine, religion, tradition, archaeological excavations have uncovered clove burnt onto the floor of a kitchen, dated to 1700 BCE, at the Mesopotamian site of Terqa, in modern-day Syria. The ancient Indian epic Ramayana mentions cloves, the Romans had cloves in the 1st century CE, as Pliny the Elder wrote about them. In the story of Genesis, Joseph was sold into slavery by his brothers to spice merchants, in the biblical poem Song of Solomon, the male speaker compares his beloved to many forms of spices. The earliest written records of spices come from ancient Egyptian, Chinese, the Ebers Papyrus from Early Egyptians that dates from 1550 B. C. E. Describes some eight hundred different medicinal remedies and numerous medicinal procedures, historians believe that nutmeg, which originates from the Banda Islands in Southeast Asia, was introduced to Europe in the 6th century BCE. Indonesian merchants traveled around China, India, the Middle East, Arab merchants facilitated the routes through the Middle East and India. This resulted in the Egyptian port city of Alexandria being the trading center for spices. The most important discovery prior to the European spice trade were the monsoon winds, sailing from Eastern spice cultivators to Western European consumers gradually replaced the land-locked spice routes once facilitated by the Middle East Arab caravans. Spices were among the most demanded and expensive available in Europe in the Middle Ages. Given medieval medicines main theory of humorism, spices and herbs were indispensable to balance humors in food, in addition to being desired by those using medieval medicine, the European elite also craved spices in the Middle Ages. An example of the European aristocracys demand for spice comes from the King of Aragon and he was specifically looking for spices to put in wine, and was not alone among European monarchs at the time to have such a desire for spice. Spices were all imported from plantations in Asia and Africa, which made them expensive, from the 8th until the 15th century, the Republic of Venice had the monopoly on spice trade with the Middle East, and along with it the neighboring Italian city-states. The trade made the region rich and it has been estimated that around 1,000 tons of pepper and 1,000 tons of the other common spices were imported into Western Europe each year during the Late Middle Ages
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Wood
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Wood is a porous and fibrous structural tissue found in the stems and roots of trees, and other woody plants. It is a material, a natural composite of cellulose fibers which are strong in tension embedded in a matrix of lignin which resists compression. Wood is sometimes defined as only the secondary xylem in the stems of trees, in a living tree it performs a support function, enabling woody plants to grow large or to stand up by themselves. It also conveys water and nutrients between the leaves, other growing tissues, and the roots, Wood may also refer to other plant materials with comparable properties, and to material engineered from wood, or wood chips or fiber. In 2005, the stock of forests worldwide was about 434 billion cubic meters. As an abundant, carbon-neutral renewable resource, woody materials have been of intense interest as a source of renewable energy, in 1991 approximately 3.5 billion cubic meters of wood were harvested. Dominant uses were for furniture and building construction, a 2011 discovery in the Canadian province of New Brunswick discovered the earliest known plants to have grown wood, approximately 395 to 400 million years ago. Wood can be dated by carbon dating and in species by dendrochronology to make inferences about when a wooden object was created. People have used wood for millennia for many purposes, primarily as a fuel or as a material for making houses, tools, weapons, furniture, packaging, artworks. Constructions using wood date back ten thousand years, buildings like the European Neolithic long house were made primarily of wood. Recent use of wood has changed by the addition of steel. The year-to-year variation in tree-ring widths and isotopic abundances gives clues to the climate at that time. This process is known as growth, it is the result of cell division in the vascular cambium, a lateral meristem. These cells then go on to form thickened secondary cell walls, composed mainly of cellulose, hemicellulose, if the distinctiveness between seasons is annual, these growth rings are referred to as annual rings. Where there is little seasonal difference growth rings are likely to be indistinct or absent, if the bark of the tree has been removed in a particular area, the rings will likely be deformed as the plant overgrows the scar. It is usually lighter in color than that near the portion of the ring. The outer portion formed later in the season is known as the latewood or summerwood. However, there are differences, depending on the kind of wood
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