1.
Jmol
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Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool and it is written in the programming language Java, so it can run on the operating systems Windows, macOS, Linux, and Unix, if Java is installed. It is free and open-source software released under a GNU Lesser General Public License version 2.0, a standalone application and a software development kit exist that can be integrated into other Java applications, such as Bioclipse and Taverna. A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways, for example, molecules can be displayed as ball-and-stick models, space-filling models, ribbon diagrams, etc. Jmol supports a range of chemical file formats, including Protein Data Bank, Crystallographic Information File, MDL Molfile. There is also a JavaScript-only version, JSmol, that can be used on computers with no Java, the Jmol applet, among other abilities, offers an alternative to the Chime plug-in, which is no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS9. Jmol requires Java installation and operates on a variety of platforms. For example, Jmol is fully functional in Mozilla Firefox, Internet Explorer, Opera, Google Chrome, fast and Scriptable Molecular Graphics in Web Browsers without Java3D
2.
ChEMBL
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ChEMBL or ChEMBLdb is a manually curated chemical database of bioactive molecules with drug-like properties. It is maintained by the European Bioinformatics Institute, of the European Molecular Biology Laboratory, based at the Wellcome Trust Genome Campus, Hinxton, the database, originally known as StARlite, was developed by a biotechnology company called Inpharmatica Ltd. later acquired by Galapagos NV. The data was acquired for EMBL in 2008 with an award from The Wellcome Trust, resulting in the creation of the ChEMBL chemogenomics group at EMBL-EBI, the ChEMBL database contains compound bioactivity data against drug targets. Bioactivity is reported in Ki, Kd, IC50, and EC50, data can be filtered and analyzed to develop compound screening libraries for lead identification during drug discovery. ChEMBL version 2 was launched in January 2010, including 2.4 million bioassay measurements covering 622,824 compounds and this was obtained from curating over 34,000 publications across twelve medicinal chemistry journals. ChEMBLs coverage of available bioactivity data has grown to become the most comprehensive ever seen in a public database, in October 2010 ChEMBL version 8 was launched, with over 2.97 million bioassay measurements covering 636,269 compounds. ChEMBL_10 saw the addition of the PubChem confirmatory assays, in order to integrate data that is comparable to the type, ChEMBLdb can be accessed via a web interface or downloaded by File Transfer Protocol. It is formatted in a manner amenable to computerized data mining, ChEMBL is also integrated into other large-scale chemistry resources, including PubChem and the ChemSpider system of the Royal Society of Chemistry. In addition to the database, the ChEMBL group have developed tools and these include Kinase SARfari, an integrated chemogenomics workbench focussed on kinases. The system incorporates and links sequence, structure, compounds and screening data, the primary purpose of ChEMBL-NTD is to provide a freely accessible and permanent archive and distribution centre for deposited data. July 2012 saw the release of a new data service, sponsored by the Medicines for Malaria Venture. The data in this service includes compounds from the Malaria Box screening set, myChEMBL, the ChEMBL virtual machine, was released in October 2013 to allow users to access a complete and free, easy-to-install cheminformatics infrastructure. In December 2013, the operations of the SureChem patent informatics database were transferred to EMBL-EBI, in a portmanteau, SureChem was renamed SureChEMBL. 2014 saw the introduction of the new resource ADME SARfari - a tool for predicting and comparing cross-species ADME targets
3.
ChemSpider
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ChemSpider is a database of chemicals. ChemSpider is owned by the Royal Society of Chemistry, the database contains information on more than 50 million molecules from over 500 data sources including, Each chemical is given a unique identifier, which forms part of a corresponding URL. This is an approach to develop an online chemistry database. The search can be used to widen or restrict already found results, structure searching on mobile devices can be done using free apps for iOS and for the Android. The ChemSpider database has been used in combination with text mining as the basis of document markup. The result is a system between chemistry documents and information look-up via ChemSpider into over 150 data sources. ChemSpider was acquired by the Royal Society of Chemistry in May,2009, prior to the acquisition by RSC, ChemSpider was controlled by a private corporation, ChemZoo Inc. The system was first launched in March 2007 in a release form. ChemSpider has expanded the generic support of a database to include support of the Wikipedia chemical structure collection via their WiChempedia implementation. A number of services are available online. SyntheticPages is an interactive database of synthetic chemistry procedures operated by the Royal Society of Chemistry. Users submit synthetic procedures which they have conducted themselves for publication on the site and these procedures may be original works, but they are more often based on literature reactions. Citations to the published procedure are made where appropriate. They are checked by an editor before posting. The pages do not undergo formal peer-review like a journal article. The comments are moderated by scientific editors. The intention is to collect practical experience of how to conduct useful chemical synthesis in the lab, while experimental methods published in an ordinary academic journal are listed formally and concisely, the procedures in ChemSpider SyntheticPages are given with more practical detail. Comments by submitters are included as well, other publications with comparable amounts of detail include Organic Syntheses and Inorganic Syntheses
4.
European Chemicals Agency
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ECHA is the driving force among regulatory authorities in implementing the EUs chemicals legislation. ECHA helps companies to comply with the legislation, advances the safe use of chemicals, provides information on chemicals and it is located in Helsinki, Finland. The Agency, headed by Executive Director Geert Dancet, started working on 1 June 2007, the REACH Regulation requires companies to provide information on the hazards, risks and safe use of chemical substances that they manufacture or import. Companies register this information with ECHA and it is freely available on their website. So far, thousands of the most hazardous and the most commonly used substances have been registered, the information is technical but gives detail on the impact of each chemical on people and the environment. This also gives European consumers the right to ask whether the goods they buy contain dangerous substances. The Classification, Labelling and Packaging Regulation introduces a globally harmonised system for classifying and labelling chemicals into the EU. This worldwide system makes it easier for workers and consumers to know the effects of chemicals, companies need to notify ECHA of the classification and labelling of their chemicals. So far, ECHA has received over 5 million notifications for more than 100000 substances, the information is freely available on their website. Consumers can check chemicals in the products they use, Biocidal products include, for example, insect repellents and disinfectants used in hospitals. The Biocidal Products Regulation ensures that there is information about these products so that consumers can use them safely. ECHA is responsible for implementing the regulation, the law on Prior Informed Consent sets guidelines for the export and import of hazardous chemicals. Through this mechanism, countries due to hazardous chemicals are informed in advance and have the possibility of rejecting their import. Substances that may have effects on human health and the environment are identified as Substances of Very High Concern 1. These are mainly substances which cause cancer, mutation or are toxic to reproduction as well as substances which persist in the body or the environment, other substances considered as SVHCs include, for example, endocrine disrupting chemicals. Companies manufacturing or importing articles containing these substances in a concentration above 0 and they are required to inform users about the presence of the substance and therefore how to use it safely. Consumers have the right to ask the retailer whether these substances are present in the products they buy, once a substance has been officially identified in the EU as being of very high concern, it will be added to a list. This list is available on ECHA’s website and shows consumers and industry which chemicals are identified as SVHCs, Substances placed on the Candidate List can then move to another list
5.
PubChem
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PubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information, a component of the National Library of Medicine, PubChem can be accessed for free through a web user interface. Millions of compound structures and descriptive datasets can be downloaded via FTP. PubChem contains substance descriptions and small molecules with fewer than 1000 atoms and 1000 bonds, more than 80 database vendors contribute to the growing PubChem database. PubChem consists of three dynamically growing primary databases, as of 28 January 2016, Compounds,82.6 million entries, contains pure and characterized chemical compounds. Substances,198 million entries, contains also mixtures, extracts, complexes, bioAssay, bioactivity results from 1.1 million high-throughput screening programs with several million values. PubChem contains its own online molecule editor with SMILES/SMARTS and InChI support that allows the import and export of all common chemical file formats to search for structures and fragments. In the text search form the database fields can be searched by adding the name in square brackets to the search term. A numeric range is represented by two separated by a colon. The search terms and field names are case-insensitive, parentheses and the logical operators AND, OR, and NOT can be used. AND is assumed if no operator is used, example,0,5000,50,10 -5,5 PubChem was released in 2004. The American Chemical Society has raised concerns about the publicly supported PubChem database and they have a strong interest in the issue since the Chemical Abstracts Service generates a large percentage of the societys revenue. To advocate their position against the PubChem database, ACS has actively lobbied the US Congress, soon after PubChems creation, the American Chemical Society lobbied U. S. Congress to restrict the operation of PubChem, which they asserted competes with their Chemical Abstracts Service
6.
International Chemical Identifier
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Initially developed by IUPAC and NIST from 2000 to 2005, the format and algorithms are non-proprietary. The continuing development of the standard has supported since 2010 by the not-for-profit InChI Trust. The current version is 1.04 and was released in September 2011, prior to 1.04, the software was freely available under the open source LGPL license, but it now uses a custom license called IUPAC-InChI Trust License. Not all layers have to be provided, for instance, the layer can be omitted if that type of information is not relevant to the particular application. InChIs can thus be seen as akin to a general and extremely formalized version of IUPAC names and they can express more information than the simpler SMILES notation and differ in that every structure has a unique InChI string, which is important in database applications. Information about the 3-dimensional coordinates of atoms is not represented in InChI, the InChI algorithm converts input structural information into a unique InChI identifier in a three-step process, normalization, canonicalization, and serialization. The InChIKey, sometimes referred to as a hashed InChI, is a fixed length condensed digital representation of the InChI that is not human-understandable. The InChIKey specification was released in September 2007 in order to facilitate web searches for chemical compounds and it should be noted that, unlike the InChI, the InChIKey is not unique, though collisions can be calculated to be very rare, they happen. In January 2009 the final 1.02 version of the InChI software was released and this provided a means to generate so called standard InChI, which does not allow for user selectable options in dealing with the stereochemistry and tautomeric layers of the InChI string. The standard InChIKey is then the hashed version of the standard InChI string, the standard InChI will simplify comparison of InChI strings and keys generated by different groups, and subsequently accessed via diverse sources such as databases and web resources. Every InChI starts with the string InChI= followed by the version number and this is followed by the letter S for standard InChIs. The remaining information is structured as a sequence of layers and sub-layers, the layers and sub-layers are separated by the delimiter / and start with a characteristic prefix letter. The six layers with important sublayers are, Main layer Chemical formula and this is the only sublayer that must occur in every InChI. The atoms in the formula are numbered in sequence, this sublayer describes which atoms are connected by bonds to which other ones. Describes how many hydrogen atoms are connected to each of the other atoms, the condensed,27 character standard InChIKey is a hashed version of the full standard InChI, designed to allow for easy web searches of chemical compounds. Most chemical structures on the Web up to 2007 have been represented as GIF files, the full InChI turned out to be too lengthy for easy searching, and therefore the InChIKey was developed. With all databases currently having below 50 million structures, such duplication appears unlikely at present, a recent study more extensively studies the collision rate finding that the experimental collision rate is in agreement with the theoretical expectations. Example, Morphine has the structure shown on the right, as the InChI cannot be reconstructed from the InChIKey, an InChIKey always needs to be linked to the original InChI to get back to the original structure
7.
Simplified molecular-input line-entry system
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The simplified molecular-input line-entry system is a specification in form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules, the original SMILES specification was initiated in the 1980s. It has since modified and extended. In 2007, a standard called OpenSMILES was developed in the open-source chemistry community. Other linear notations include the Wiswesser Line Notation, ROSDAL and SLN, the original SMILES specification was initiated by David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s. The Environmental Protection Agency funded the project to develop SMILES. It has since modified and extended by others, most notably by Daylight Chemical Information Systems. In 2007, a standard called OpenSMILES was developed by the Blue Obelisk open-source chemistry community. Other linear notations include the Wiswesser Line Notation, ROSDAL and SLN, in July 2006, the IUPAC introduced the InChI as a standard for formula representation. SMILES is generally considered to have the advantage of being slightly more human-readable than InChI, the term SMILES refers to a line notation for encoding molecular structures and specific instances should strictly be called SMILES strings. However, the term SMILES is also used to refer to both a single SMILES string and a number of SMILES strings, the exact meaning is usually apparent from the context. The terms canonical and isomeric can lead to confusion when applied to SMILES. The terms describe different attributes of SMILES strings and are not mutually exclusive, typically, a number of equally valid SMILES strings can be written for a molecule. For example, CCO, OCC and CC all specify the structure of ethanol, algorithms have been developed to generate the same SMILES string for a given molecule, of the many possible strings, these algorithms choose only one of them. This SMILES is unique for each structure, although dependent on the algorithm used to generate it. These algorithms first convert the SMILES to a representation of the molecular structure. A common application of canonical SMILES is indexing and ensuring uniqueness of molecules in a database, there is currently no systematic comparison across commercial software to test if such flaws exist in those packages. SMILES notation allows the specification of configuration at tetrahedral centers, and these are structural features that cannot be specified by connectivity alone and SMILES which encode this information are termed isomeric SMILES
8.
Chemical formula
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These are limited to a single typographic line of symbols, which may include subscripts and superscripts. A chemical formula is not a name, and it contains no words. Although a chemical formula may imply certain simple chemical structures, it is not the same as a full chemical structural formula. Chemical formulas can fully specify the structure of only the simplest of molecules and chemical substances, the simplest types of chemical formulas are called empirical formulas, which use letters and numbers indicating the numerical proportions of atoms of each type. Molecular formulas indicate the numbers of each type of atom in a molecule. For example, the formula for glucose is CH2O, while its molecular formula is C6H12O6. This is possible if the relevant bonding is easy to show in one dimension, an example is the condensed molecular/chemical formula for ethanol, which is CH3-CH2-OH or CH3CH2OH. For reasons of structural complexity, there is no condensed chemical formula that specifies glucose, chemical formulas may be used in chemical equations to describe chemical reactions and other chemical transformations, such as the dissolving of ionic compounds into solution. A chemical formula identifies each constituent element by its chemical symbol, in empirical formulas, these proportions begin with a key element and then assign numbers of atoms of the other elements in the compound, as ratios to the key element. For molecular compounds, these numbers can all be expressed as whole numbers. For example, the formula of ethanol may be written C2H6O because the molecules of ethanol all contain two carbon atoms, six hydrogen atoms, and one oxygen atom. Some types of compounds, however, cannot be written with entirely whole-number empirical formulas. An example is boron carbide, whose formula of CBn is a variable non-whole number ratio with n ranging from over 4 to more than 6.5. When the chemical compound of the consists of simple molecules. These types of formulas are known as molecular formulas and condensed formulas. A molecular formula enumerates the number of atoms to reflect those in the molecule, so that the formula for glucose is C6H12O6 rather than the glucose empirical formula. However, except for very simple substances, molecular chemical formulas lack needed structural information, for simple molecules, a condensed formula is a type of chemical formula that may fully imply a correct structural formula. For example, ethanol may be represented by the chemical formula CH3CH2OH
9.
Melting point
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The melting point of a solid is the temperature at which it changes state from solid to liquid at atmospheric pressure. At the melting point the solid and liquid phase exist in equilibrium, the melting point of a substance depends on pressure and is usually specified at standard pressure. When considered as the temperature of the change from liquid to solid. Because of the ability of some substances to supercool, the point is not considered as a characteristic property of a substance. For most substances, melting and freezing points are approximately equal, for example, the melting point and freezing point of mercury is 234.32 kelvins. However, certain substances possess differing solid-liquid transition temperatures, for example, agar melts at 85 °C and solidifies from 31 °C to 40 °C, such direction dependence is known as hysteresis. The melting point of ice at 1 atmosphere of pressure is close to 0 °C. In the presence of nucleating substances the freezing point of water is the same as the melting point, the chemical element with the highest melting point is tungsten, at 3687 K, this property makes tungsten excellent for use as filaments in light bulbs. Many laboratory techniques exist for the determination of melting points, a Kofler bench is a metal strip with a temperature gradient. Any substance can be placed on a section of the strip revealing its thermal behaviour at the temperature at that point, differential scanning calorimetry gives information on melting point together with its enthalpy of fusion. A basic melting point apparatus for the analysis of crystalline solids consists of an oil bath with a transparent window, the several grains of a solid are placed in a thin glass tube and partially immersed in the oil bath. The oil bath is heated and with the aid of the melting of the individual crystals at a certain temperature can be observed. In large/small devices, the sample is placed in a heating block, the measurement can also be made continuously with an operating process. For instance, oil refineries measure the point of diesel fuel online, meaning that the sample is taken from the process. This allows for more frequent measurements as the sample does not have to be manually collected, for refractory materials the extremely high melting point may be determined by heating the material in a black body furnace and measuring the black-body temperature with an optical pyrometer. For the highest melting materials, this may require extrapolation by several hundred degrees, the spectral radiance from an incandescent body is known to be a function of its temperature. An optical pyrometer matches the radiance of a body under study to the radiance of a source that has been previously calibrated as a function of temperature, in this way, the measurement of the absolute magnitude of the intensity of radiation is unnecessary. However, known temperatures must be used to determine the calibration of the pyrometer, for temperatures above the calibration range of the source, an extrapolation technique must be employed
10.
Occupational safety and health
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These terms of course also refer to the goals of this field, so their use in the sense of this article was originally an abbreviation of occupational safety and health program/department etc. The goals of occupational safety and health programs include to foster a safe, OSH may also protect co-workers, family members, employers, customers, and many others who might be affected by the workplace environment. In the United States, the occupational health and safety is referred to as occupational health and occupational and non-occupational safety. In common-law jurisdictions, employers have a common law duty to take care of the safety of their employees. As defined by the World Health Organization occupational health deals with all aspects of health, Health has been defined as a state of complete physical, mental and social well-being and not merely the absence of disease or infirmity. Occupational health is a field of healthcare concerned with enabling an individual to undertake their occupation. Health has been defined as It contrasts, for example, with the promotion of health and safety at work, since 1950, the International Labour Organization and the World Health Organization have shared a common definition of occupational health. It was adopted by the Joint ILO/WHO Committee on Occupational Health at its first session in 1950, the concept of working culture is intended in this context to mean a reflection of the essential value systems adopted by the undertaking concerned. Such a culture is reflected in practice in the systems, personnel policy, principles for participation, training policies. Professionals advise on a range of occupational health matters. The research and regulation of safety and health are a relatively recent phenomenon. As labor movements arose in response to concerns in the wake of the industrial revolution. The initial remit of the Inspectorate was to police restrictions on the hours in the textile industry of children. The commission sparked public outrage resulted in the Mines Act of 1842. Otto von Bismarck inaugurated the first social insurance legislation in 1883, similar acts followed in other countries, partly in response to labor unrest. Although work provides many economic and other benefits, an array of workplace hazards also present risks to the health. Personal protective equipment can protect against many of these hazards. Physical hazards affect many people in the workplace, Falls are also a common cause of occupational injuries and fatalities, especially in construction, extraction, transportation, healthcare, and building cleaning and maintenance
11.
Safety data sheet
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A safety data sheet, material safety data sheet, or product safety data sheet is an important component of product stewardship, occupational safety and health, and spill-handling procedures. SDS formats can vary from source to source within a country depending on national requirements, SDSs are a widely used system for cataloging information on chemicals, chemical compounds, and chemical mixtures. SDS information may include instructions for the use and potential hazards associated with a particular material or product. The SDS should be available for reference in the area where the chemicals are being stored or in use, there is also a duty to properly label substances on the basis of physico-chemical, health and/or environmental risk. Labels can include hazard symbols such as the European Union standard symbols, a SDS for a substance is not primarily intended for use by the general consumer, focusing instead on the hazards of working with the material in an occupational setting. It is important to use an SDS specific to country and supplier, as the same product can have different formulations in different countries. The formulation and hazard of a product using a name may vary between manufacturers in the same country. Safety data sheets have made an integral part of the system of Regulation No 1907/2006. The SDS must be supplied in a language of the Member State where the substance or mixture is placed on the market. The 16 sections are, SECTION1, Identification of the substance/mixture, relevant identified uses of the substance or mixture and uses advised against 1.3. Details of the supplier of the safety data sheet 1.4, Emergency telephone number SECTION2, Hazards identification 2.1. Classification of the substance or mixture 2.2, Other hazards SECTION3, Composition/information on ingredients 3.1. Mixtures SECTION4, First aid measures 4.1, Description of first aid measures 4.2. Most important symptoms and effects, both acute and delayed 4.3, indication of any immediate medical attention and special treatment needed SECTION5, Firefighting measures 5.1. Special hazards arising from the substance or mixture 5.3, advice for firefighters SECTION6, Accidental release measure 6.1. Personal precautions, protective equipment and emergency procedures 6.2, methods and material for containment and cleaning up 6.4. Reference to other sections SECTION7, Handling and storage 7.1, conditions for safe storage, including any incompatibilities 7.3. Specific end use SECTION8, Exposure controls/personal protection 8.1, Exposure controls SECTION9, Physical and chemical properties 9.1
12.
Pharmacokinetics
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Pharmacokinetics, sometimes abbreviated as PK, is a branch of pharmacology dedicated to determining the fate of substances administered to a living organism. The substances of interest include any chemical xenobiotic such as, pharmaceutical drugs, pesticides, food additives, cosmetic ingredients, etc. It attempts to analyze chemical metabolism and to discover the fate of a chemical from the moment that it is administered up to the point at which it is eliminated from the body. Pharmacokinetics is the study of how an organism affects a drug, both together influence dosing, benefit, and adverse effects, as seen in PK/PD models. Pharmacokinetic properties of chemicals are affected by the route of administration and these may affect the absorption rate. Models have been developed to simplify conceptualization of the processes that take place in the interaction between an organism and a chemical substance. The various compartments that the model is divided into are commonly referred to as the ADME scheme, absorption - the process of a substance entering the blood circulation. Distribution - the dispersion or dissemination of substances throughout the fluids, metabolism – the recognition by the organism that a foreign substance is present and the irreversible transformation of parent compounds into daughter metabolites. Excretion - the removal of the substances from the body, in rare cases, some drugs irreversibly accumulate in body tissue. The two phases of metabolism and excretion can also be grouped together under the title elimination, the study of these distinct phases involves the use and manipulation of basic concepts in order to understand the process dynamics. All these concepts can be represented through mathematical formulas that have a graphical representation. The model outputs for a drug can be used in industry or in the application of pharmacokinetic concepts. Clinical pharmacokinetics provides many performance guidelines for effective and efficient use of drugs for human-health professionals, in practice, it is generally considered that steady state is reached when a time of 4 to 5 times the half-life for a drug after regular dosing is started. Noncompartmental methods estimate the exposure to a drug by estimating the area under the curve of a concentration-time graph, compartmental methods estimate the concentration-time graph using kinetic models. Noncompartmental methods are more versatile in that they do not assume any specific compartmental model. The final outcome of the transformations that a drug undergoes in an organism, a number of functional models have been developed in order to simplify the study of pharmacokinetics. These models are based on a consideration of an organism as a number of related compartments, the simplest idea is to think of an organism as only one homogenous compartment. However, these models do not always reflect the real situation within an organism
13.
Excretion
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Excretion is the process by which metabolic wastes and other non-useful materials are eliminated from an organism. In vertebrates this is carried out by the lungs, kidneys. This is in contrast with secretion, where the substance may have specific tasks after leaving the cell, excretion is an essential process in all forms of life. For example, in urine is expelled through the urethra. In unicellular organisms, waste products are discharged directly through the surface of the cell, green plants produce carbon dioxide and water as respiratory products. In green plants, the carbon dioxide released during respiration gets utilized during photosynthesis, oxygen is a by product generated during photosynthesis, and exits through stomata, root cell walls, and other routes. Plants can get rid of water by transpiration and guttation. These latter processes do not need added energy, they act passively, however, during the pre-abscission phase, the metabolic levels of a leaf are high. Plants also excrete some waste substances into the soil around them, in animals, the main excretory products are carbon dioxide, ammonia, urea, uric acid, guanine and creatine. The liver and kidneys clear many substances from the blood, aquatic animals usually excrete ammonia directly into the external environment, as this compound has high solubility and there is ample water available for dilution. In terrestrial animals ammonia-like compounds are converted into other materials as there is less water in the environment. Birds excrete their nitrogenous wastes as uric acid in the form of a paste and this is metabolically more expensive, but allows more efficient water retention and it can be stored more easily in the egg. Many avian species, especially seabirds, can also excrete salt via specialized nasal salt glands, in insects, a system involving Malpighian tubules is utilized to excrete metabolic waste. Metabolic waste diffuses or is actively transported into the tubule, which transports the wastes to the intestines, the metabolic waste is then released from the body along with fecal matter. The excreted material may be called dejecta or ejecta, in pathology the word ejecta is more commonly used. UAlberta. ca, Animation of excretion Brian J Ford on leaf fall in Nature
14.
Flavan-3-ol
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Flavan-3-ols are derivatives of flavans that use the 2-phenyl-3, 4-dihydro-2H-chromen-3-ol skeleton. These compounds include catechin, epicatechin gallate, epigallocatechin, epigallocatechin gallate, flavanols are not to be confused with flavonols, a class of flavonoids containing a ketone group. The single-molecule catechin, or isomer epicatechin, adds four hydroxyls to flavan-3-ol, making building blocks for concatenated polymers, flavanols possess two chiral carbons, meaning four diastereoisomers occur for each of them. Catechins are distinguished from the yellow, ketone-containing flavonoids such as quercitin and rutin, early use of the term bioflavonoid was imprecisely applied to include the flavanols, which are distinguished by absence of ketone. Catechin monomers, dimers, and trimers are colorless, higher order polymers, anthocyanidins, exhibit deepening reds and become tannins. The catechins are abundant in teas derived from the tea plant Camellia sinensis, as well as in some cocoas, catechins are also present in the human diet in fruits, vegetables and wine, and are found in many other plant species, as well as cocoa. Catechin and epicatechin are epimers, with -epicatechin and -catechin being the most common optical isomers found in nature, catechin was first isolated from the plant extract catechu, from which it derives its name. Heating catechin past its point of decomposition releases pyrocatechol, which explains the origin of the names of these compounds. Catechin gallates are gallic acid esters of the catechins, an example is epigallocatechin gallate, the flavonoids are products from a cinnamoyl-CoA starter unit, with chain extension using three molecules of malonyl-CoA. Reactions are catalyzed by a type III PKS enzyme and these enzyme do not use ACPSs, but instead employ coenzyme A esters and have a single active site to perform the necessary series of reactions, e. g. chain extension, condensation, and cyclization. Chain extension of 4-hydroxycinnamoyl-CoA with three molecules of malonyl-CoA gives initially a polyketide, which can be folded and these allow Claisen-like reactions to occur, generating aromatic rings. HSCoA, Coenzyme A. L-Tyr, L-tyrosine, L-Phe, L-phenylalanine, the supposed health benefits of catechins have been studied extensively in humans and animal models, but there are no proven effects that apply to human health. Until 2013, neither the Food and Drug Administration nor the European Food Safety Authority had approved any health claim for catechins or approved any as pharmaceutical drugs, moreover, several companies have been cautioned by the FDA over misleading health claims. Additionally, such a product is high in fat, sugar and Calories, fluorescence-lifetime imaging microscopy can be used to detect flavanols in plant cells Recent study tested catechins employed to coat nanoparticles of iron oxides in the blood. These particles allow visualization of vessels - and especially cancer tumors in mice - in an MRI exam, the nanoparticles would clump together without the catechin coating
15.
Antioxidant
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An antioxidant is a molecule that inhibits the oxidation of other molecules. Oxidation is a reaction that can produce free radicals, leading to chain reactions that may damage cells. Antioxidants such as thiols or ascorbic acid terminate these chain reactions, supplementation with selenium or vitamin E does not reduce the risk of cardiovascular disease. Oxidative stress can be considered as either a cause or consequence of some diseases, industrial antioxidants have diverse uses, such as food and cosmetics preservatives and inhibitors of rubber or gasoline deterioration. Although certain levels of antioxidant vitamins in the diet are required for good health, moreover, if they are actually beneficial, it is unknown which antioxidant are needed from the diet and in what amounts beyond typical dietary intake. Some authors dispute the hypothesis that antioxidant vitamins could prevent chronic diseases, polyphenols, which often have antioxidant properties in vitro, are not necessarily antioxidants in vivo due to extensive metabolism. In many polyphenols, the group acts as electron acceptor and is therefore responsible for the antioxidant activity. However, this catechol group undergoes extensive metabolism upon uptake in the body, for example by catechol-O-methyl transferase. Many polyphenols may have non-antioxidant roles in minute concentrations that affect cell-to-cell signaling, receptor sensitivity, tirilazad is an antioxidant steroid derivative that inhibits the lipid peroxidation that is believed to play a key role in neuronal death in stroke and head injury. It demonstrated activity in animal models of stroke, but human trials demonstrated no effect on mortality or other outcomes in subarachnoid haemorrhage, similarly, the designed antioxidant NXY-059 exhibited efficacy in animal models, but failed to improve stroke outcomes in a clinical trial. As of November 2014, other antioxidants are being studied as potential neuroprotectants, common pharmaceuticals with antioxidant properties may interfere with the efficacy of certain anticancer medication and radiation. During exercise, oxygen consumption can increase by a factor of more than 10, however, no benefits for physical performance to athletes are seen with vitamin E supplementation and 6 weeks of vitamin E supplementation had no effect on muscle damage in ultramarathon runners. Some research suggests that supplementation with amounts as high as 1000 mg of vitamin C inhibits recovery, other studies indicated that antioxidant supplementation may attenuate the cardiovascular benefits of exercise. Relatively strong reducing acids can have antinutrient effects by binding to dietary minerals such as iron and zinc in the gastrointestinal tract, notable examples are oxalic acid, tannins and phytic acid, which are high in plant-based diets. Calcium and iron deficiencies are not uncommon in diets in developing countries where meat is eaten and there is high consumption of phytic acid from beans. Nonpolar antioxidants such as major component of oil of cloves—have toxicity limits that can be exceeded with the misuse of undiluted essential oils. Toxicity associated with high doses of water-soluble antioxidants such as ascorbic acid are less of a concern, more seriously, very high doses of some antioxidants may have harmful long-term effects. The beta-carotene and Retinol Efficacy Trial study of cancer patients found that smokers given supplements containing beta-carotene
16.
Plant
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Plants are mainly multicellular, predominantly photosynthetic eukaryotes of the kingdom Plantae. The term is generally limited to the green plants, which form an unranked clade Viridiplantae. This includes the plants, conifers and other gymnosperms, ferns, clubmosses, hornworts, liverworts, mosses and the green algae. Green plants have cell walls containing cellulose and obtain most of their energy from sunlight via photosynthesis by primary chloroplasts and their chloroplasts contain chlorophylls a and b, which gives them their green color. Some plants are parasitic and have lost the ability to produce amounts of chlorophyll or to photosynthesize. Plants are characterized by sexual reproduction and alternation of generations, although reproduction is also common. There are about 300–315 thousand species of plants, of which the great majority, green plants provide most of the worlds molecular oxygen and are the basis of most of Earths ecologies, especially on land. Plants that produce grains, fruits and vegetables form humankinds basic foodstuffs, Plants play many roles in culture. They are used as ornaments and, until recently and in variety, they have served as the source of most medicines. The scientific study of plants is known as botany, a branch of biology, Plants are one of the two groups into which all living things were traditionally divided, the other is animals. The division goes back at least as far as Aristotle, who distinguished between plants, which generally do not move, and animals, which often are mobile to catch their food. Much later, when Linnaeus created the basis of the system of scientific classification. Since then, it has become clear that the plant kingdom as originally defined included several unrelated groups, however, these organisms are still often considered plants, particularly in popular contexts. When the name Plantae or plant is applied to a group of organisms or taxon. The evolutionary history of plants is not yet settled. Those which have been called plants are in bold, the way in which the groups of green algae are combined and named varies considerably between authors. Algae comprise several different groups of organisms which produce energy through photosynthesis, most conspicuous among the algae are the seaweeds, multicellular algae that may roughly resemble land plants, but are classified among the brown, red and green algae. Each of these groups also includes various microscopic and single-celled organisms
17.
Flavonoid
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Flavonoids are a class of plant and fungus secondary metabolites. Chemically, flavonoids have the structure of a 15-carbon skeleton. This carbon structure can be abbreviated C6-C3-C6 and this class was the first to be termed bioflavonoids. The terms flavonoid and bioflavonoid have also more loosely used to describe non-ketone polyhydroxy polyphenol compounds which are more specifically termed flavanoids. The three cycle or heterocycles in the backbone are generally called ring A, B and C. Ring A usually shows a phloroglucinol substitution pattern, Flavonoids are widely distributed in plants, fulfilling many functions. Flavonoids are the most important plant pigments for coloration, producing yellow or red/blue pigmentation in petals designed to attract pollinator animals. In higher plants, flavonoids are involved in UV filtration, symbiotic nitrogen fixation and they may also act as chemical messengers, physiological regulators, and cell cycle inhibitors. Flavonoids secreted by the root of their host plant help Rhizobia in the stage of their symbiotic relationship with legumes like peas, beans, clover. In addition, some flavonoids have inhibitory activity against organisms that cause plant diseases, over 5000 naturally occurring flavonoids have been characterized from various plants. Flavonols, the original such as quercetin, are also found ubiquitously. Further information on sources of flavonoids can be obtained from the US Department of Agriculture flavonoid database. Parsley, both fresh and dried, contains flavones, blueberries are a dietary source of anthocyanidins. Black tea is a source of dietary flavan-3-ols. The citrus flavonoids include hesperidin, quercitrin, rutin, and the flavone tangeritin, Flavonoids exist naturally in cocoa, but because they can be bitter, they are often removed from chocolate, even dark chocolate. Although flavonoids are present in milk chocolate, milk may interfere with their absorption, peanut skin contains significant polyphenol content, including flavonoids. Food composition data for flavonoids were provided by the USDA database on flavonoids, in the United States NHANES survey, mean flavonoid intake was 190 mg/d in adults, with flavan-3-ols as the main contributor. In the European Union, based on data from EFSA, mean flavonoid intake was 140 mg/d, the main type of flavonoids consumed in the EU and USA were flavan-3-ols, mainly from tea, while intake of other flavonoids was considerably lower
18.
Catechu
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Catechu is an extract of acacia trees used variously as a food additive, astringent, tannin, and dye. It is extracted from several species of Acacia, but especially Senegalia catechu, by boiling the wood in water and evaporating the resulting brew. It is also known as cutch, black cutch, cachou, cashoo, khoyer, terra Japonica, or Japan earth, and also katha in Hindi, kaath in Marathi, khoyer in Assamese and Bengali, and kachu in Malay. As an astringent it has used since ancient times in Ayurvedic medicine as well as in breath-freshening spice mixtures—for example in France. It is also an important ingredient in South Asian cooking paan mixtures, such as ready-made paan masala, the catechu mixture is high in natural vegetable tannins, and may be used for the tanning of animal hides. Early research by Sir Humphry Davy in the early 19th century first demonstrated the use of catechu in tanning over more expensive, under the name cutch, it is a brown dye used for tanning and dyeing and for preserving fishing nets and sails. Cutch will dye wool, silk, and cotton a yellowish-brown, cutch gives gray-browns with an iron mordant and olive-browns with a copper mordant. Black catechu has recently also been utilized by Blavod Drinks Ltd. to dye their vodka black, white cutch, also known as gambier, gambeer, or gambir, which is extracted from Uncaria gambir has the same uses. The catechu extract gave its name to the catechin and catechol chemical families first derived from it, arid Forest Research Institute An OCRd version of the US Dispensatory by Remington and Wood,1918
19.
Senegalia catechu
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Senegalia catechu is a deciduous, thorny tree which grows up to 15 m in height. The plant is called khair in Hindi, and kachu in Malay, hence the name was Latinized to catechu in Linnaean taxonomy, as the type-species from which the extracts cutch and catechu are derived. Common names for it include kher, catechu, cachou, cutchtree, black cutch, Senegalia catechu is found in Asia, China, India and the Indian Ocean area. Through derivatives of the flavanols in its extracts, the species has lent its name to the important catechins, catechols and catecholamines of chemistry, the trees seeds are a good source of protein. Kattha, an extract of its heartwood, is used as an ingredient to give red color, paan is an Indian and Southeast Asian tradition of chewing betel leaf with areca nut and slaked lime paste. Branches of the tree are quite often cut for fodder and are sometimes fed to cattle. The heart wood and bark of the tree are used in traditional medicine, a wood extract called catechu is used in traditional medicine for sore throats and diarrhea. The concentrated aqueous extract, known as gum or cutch, is astringent. It is used in Ayurvedic medicine, in ayurveda, it is used for rasayana. It is also used for its actions like anti-dyslipidemic, anthelminthic, anti-inflammatory, anti-diuretic, anti-pruritic, coolant, taste promoting, enhancing digestion and it is also used as a teeth cleaning twig, with some sources naming it the original such twig. The tree is planted for use as firewood and charcoal and its wood is highly valued for furniture. The wood has a density of about 0.88 g/cm3 and its heartwood extract is used in dyeing and leather tanning, as a preservative for fishing nets, and as a viscosity regulator for oil drilling. The tree can be propagated by planting its seeds, which are soaked in hot water first, after about six months in a nursery, the seedlings can be planted in the field. Arid Forest Research Institute Catechu Catechin Pyrocatechol Media related to Senegalia catechu at Wikimedia Commons Data related to Acacia catechu at Wikispecies
20.
Dihydropyran
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Dihydropyran is a heterocyclic compound with the formula C5H8O. The six-membered, non-aromatic ring has five carbon atoms and one oxygen atom, there are two isomers of dihydropyran that differ by the location of the double bond. 3, 4-Dihydro-2H-pyran has a bond at position 5,3. In IUPAC names, dihydro refers to the two added hydrogen atoms needed to remove one double bond from the parent compound pyran, the numbers in front of the prefix indicate the position of the added hydrogen atoms. The italicized capital H denotes the indicated hydrogen, that is a hydrogen atom present on the location where no double bond is present. The indicated hydrogen is placed just in front of the parent hydride, note that the position numbers of the ring-members not follow the position of the double bonds here. If also the double bond is removed by two more hydrogen atoms we get tetrahydropyran, or oxane. 3, 4-Dihydropyran, also known as 2, 3-dihydropyran, is used for protecting several chemicals, dihydropyran is prepared by the dehydration of tetrahydrofurfuryl alcohol over alumina at 300–400 °C. In organic synthesis, the 2-tetrahydropyranyl group is used as a group for alcohols. Reaction of the alcohol with dihydropyran forms an ether, protecting the alcohol from a variety of reactions. The alcohol can later be restored readily by acidic hydrolysis with formation of 5-hydroxypentanal
21.
Resorcinol
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It is the 1, 3-isomer of benzenediol with the formula C6H42. Benzene-1, 3-diol is the name recommended by the International Union of Pure and it is produced when any of a large number of resins are melted with potassium hydroxide, or by the distillation of Brazilwood extract. Many ortho- and para-compounds of the series also yield resorcinol on fusion with potassium hydroxide. Resorcinol crystallizes from benzene as colorless needles that are soluble in water, alcohol, and ether. It reduces Fehlings solution and ammoniacal silver solutions and it does not form a precipitate with lead acetate solution, as does the isomeric pyrocatechol. Iron chloride colors its aqueous solution a dark-violet, and bromine water precipitates tribromoresorcin and these properties are what give it its use as a colouring agent for certain chromatography experiments. It condenses with acids or acid chlorides, in the presence of dehydrating agents, to oxyketones, e. g. with zinc chloride, with the anhydrides of dibasic acids, it yields fluoresceins. When heated with calcium chloride—ammonia to 200 °C it yields meta-dioxydiphenylamine, with sodium nitrite it forms a water-soluble blue dye, which is turned red by acids, and is used as an indicator, under the name of lacmoid. It condenses readily with aldehydes, yielding with formaldehyde, on the addition of hydrochloric acid. Reaction with chloral hydrate in the presence of potassium bisulfate yields the lactone of tetra-oxydiphenyl methane carboxylic acid, in alcoholic solution it condenses with sodium acetoacetate to form 4-methylumbelliferone. In addition to electrophilic addition, resorcinol undergo nucleophilic substitution via the enone form. With concentrated nitric acid, in the presence of concentrated sulfuric acid, it yields trinitro-resorcin. Resorcinol is one of the natural phenols in argan oil. Parts of a molecule of catechin, another natural compound that is present in tea, has the skeleton structure in it. Alkylresorcinols are a marker of whole grain diet, 4-Hexylresorcinol is an anesthetic found in throat losenges. It is present in over-the-counter topical acne treatments at 2% or less concentration, weak, watery solutions of resorcinol are useful in allaying the itching in erythematous eczema. A 2% solution used as a spray has been used with marked effect in hay fever, in the latter disease 0.6 mL of the 2% solution has been given internally. It can be included as an agent in shampoo or in sunscreen cosmetics
22.
Catechol
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Catechol, also known as pyrocatechol or 1, 2-dihydroxybenzene, is an organic compound with the molecular formula C6H42. It is the isomer of the three isomeric benzenediols. This colorless compound occurs naturally in trace amounts and it was first discovered by destructive distillation of the plant extract catechin. About 20 million kg are now produced annually as a commodity organic chemical, mainly as a precursor to pesticides, flavors. Catechol occurs as white crystals that are very rapidly soluble in water. Upon heating catechin above its point, a substance that Reinsch first named Brenz-Katechusäure sublimated as a white efflorescence. This was a thermal decomposition product of the flavanols in catechin, in 1841, both Wackenroder and Zwenger independently rediscovered catechol, in reporting on their findings, Philosophical Magazine coined the name pyrocatechin. In 1879, the Journal of the Chemical Society recommended that catechol be called catechol, Catechol has since been shown to occur in free-form naturally in kino and in beechwood tar. Its sulfonic acid has been detected in the urine of horses, Catechol is produced industrially by the hydroxylation of phenol using hydrogen peroxide. Its methyl ether derivative, guaiacol, converts to catechol via hydrolysis of the CH3-O bond as promoted by hydriodic acid, like other difunctional benzene derivatives, catechol readily condenses to form heterocyclic compounds. Catechol is the acid of a chelating agent used widely in coordination chemistry. Basic solutions of catechol react with iron to give the red 3−, ferric chloride gives a green coloration with the aqueous solution, while the alkaline solution rapidly changes to a green and finally to a black color on exposure to the air. Iron-containing dioxygenase enzymes catalyze the cleavage of catechol, Catechol is produced by a reversible two-electron, two-proton reduction of 1, 2-benzoquinone. The redox series catecholate dianion, monoanionic semiquinonate, and benzoquinone are collectively called dioxolenes, small amounts of catechol occur naturally in fruits and vegetables, along with the enzyme polyphenol oxidase. Upon mixing the enzyme with the substrate and exposure to oxygen, the enzyme is inactivated by adding an acid, such as lemon juice. Excluding oxygen also prevents the browning reaction, however, the activity of the enzyme increases in cooler temperatures. Benzoquinone is said to be antimicrobial, which slows the spoilage of wounded fruits and it is one of the main natural phenols in argan oil. Pyrocatechol is also found in Agaricus bisporus and it is also a component of castoreum, a substance from the castor gland of beavers, used in perfumery
23.
Chirality (chemistry)
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Chirality /kaɪˈrælɪti/ is a geometric property of some molecules and ions. A chiral molecule/ion is non-superposable on its mirror image, the presence of an asymmetric carbon center is one of several structural features that induce chirality in organic and inorganic molecules. The term chirality is derived from the Greek word for hand, the mirror images of a chiral molecule/ion are called enantiomers or optical isomers. Individual enantiomers are often designated as either right- or left-handed, Chirality is an essential consideration when discussing the stereochemistry in organic and inorganic chemistry. The concept is of practical importance because most biomolecules and pharmaceuticals are chiral. Chirality is based on molecular symmetry elements, specifically, a chiral compound can contain no improper axis of rotation, which includes planes of symmetry and inversion center. Chiral molecules are always dissymmetric but not always asymmetric, in general, chiral molecules have point chirality at a single stereogenic atom, which has four different substituents. The two enantiomers of such compounds are said to have different absolute configurations at this center, the stereogenic atom is usually carbon, as in many biological molecules. However chirality can exist in any atom, including metals, phosphorus, Chiral nitrogen is equally possible, although the effects of nitrogen inversion can make many of these compounds impossible to isolate. While the presence of a stereogenic atom describes the great majority of cases, for instance it is not necessary for the chiral substance to have a stereogenic atom. Examples include 1-bromo-1-chloro-1-fluoroadamantane, methylethylphenyltetrahedrane, certain calixarenes and fullerenes, which have inherent chirality, the C2-symmetric species 1, 1-bi-2-naphthol,1, 3-dichloro-allene have axial chirality. -cyclooctene and many ferrocenes have planar chirality, when the optical rotation for an enantiomer is too low for practical measurement, the species is said to exhibit cryptochirality. Even isotopic differences must be considered when examining chirality, illustrative is the derivative of benzyl alcohol PhCHDOH is chiral. The S enantiomer has D = +0. 715°, many biologically active molecules are chiral, including the naturally occurring amino acids and sugars. In biological systems, most of these compounds are of the chirality, most amino acids are levorotatory. Typical naturally occurring proteins, made of L amino acids, are known as left-handed proteins, d-amino acids are very rare in nature and have only been found in small peptides attached to bacteria cell walls. The origin of this homochirality in biology is the subject of much debate, however, there is some suggestion that early amino acids could have formed in comet dust. Enzymes, which are chiral, often distinguish between the two enantiomers of a chiral substrate, one could imagine an enzyme as having a glove-like cavity that binds a substrate
24.
Stereoisomerism
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Stereoisomers are isomeric molecules that have the same molecular formula and sequence of bonded atoms, but differ in the three-dimensional orientations of their atoms in space. This contrasts with structural isomers, which share the same molecular formula, by definition, molecules that are stereoisomers of each other represent the same structural isomer. Enantiomers, also known as optical isomers, are two stereoisomers that are related to other by a reflection, They are mirror images of each other that are non-superimposable. Human hands are an analog of stereoisomerism. Every stereogenic center in one has the configuration in the other. As a result, different enantiomers of a compound may have different biological effects. Pure enantiomers also exhibit the phenomenon of optical activity and can be separated only with the use of a chiral agent, in nature, only one enantiomer of most chiral biological compounds, such as amino acids, is present. Diastereomers are stereoisomers not related through a reflection operation and they are not mirror images of each other. These include meso compounds, cis–trans isomers, and non-enantiomeric optical isomers, diastereomers seldom have the same physical properties. In the example shown below, the form of tartaric acid forms a diastereomeric pair with both levo and dextro tartaric acids, which form an enantiomeric pair. Please refer to Chirality for more regarding the D- and L- labels. Stereoisomerism about double bonds arises because rotation about the bond is restricted. The simplest examples of cis-trans isomerism are the 1, 2-disubstituted ethenes, molecule I is cis-1, 2-dichloroethene and molecule II is trans-1, 2-dichloroethene. Due to occasional ambiguity, IUPAC adopted a rigorous system wherein the substituents at each end of the double bond are assigned priority based on their atomic number. If the high-priority substituents are on the side of the bond. If they are on sides, it is E. Since chlorine has an atomic number than hydrogen, it is the highest-priority group. Using this notation to name the above pictured molecules, molecule I is -1, 2-dichloroethene and molecule II is -1 and it is not the case that Z and cis or E and trans are always interchangeable
25.
Proanthocyanidin
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Proanthocyanidins are a class of polyphenols found in a variety of plants. Many are oligomers of catechin and epicatechin and their gallic acid esters, more complex polyphenols, having the same polymeric building block, form the group of tannins. Proanthocyanidins were discovered in 1947 by Jacques Masquelier, who developed and patented techniques for the extraction of oligomeric proanthocyanidins from pine bark, however, bilberry, cranberry, black currant, green tea, black tea, and other plants also contain these flavonoids. Cocoa beans contain the highest concentrations, proanthocyanidins also may be isolated from Quercus petraea and Q. robur heartwood. Açaí oil, obtained from the fruit of the palm, is rich in numerous procyanidin oligomers. Apples contain on average per serving about eight times the amount of found in wine, with some of the highest amounts found in the Red Delicious. An extract of maritime pine bark called Pycnogenol bears 65-75 percent proanthocyanidins, thus a 100 mg serving would contain 65 to 75 mg of proanthocyanidins. Proanthocyanidin glycosides can be isolated from cocoa liquor, the seed testas of field beans contain proanthocyanidins that affect the digestibility in piglets and could have an inhibitory activity on enzymes. Cistus salviifolius also contains oligomeric proanthocyanidins, condensed tannins may be characterised by a number of techniques including depolymerisation, asymmetric flow field flow fractionation or small-angle X-ray scattering. DMACA is a dye that is useful for localization of proanthocyanidin compounds in plant histology. The use of the reagent results in blue staining and it can also be used to titrate proanthocyanidins. Proanthocyanidins from field beans or barley have been estimated using the vanillin-HCl method, proanthocyanidins can be titrated using the Procyanidolic Index. It is a method that measures the change in color when the product is mixed with certain chemicals. The greater the changes, the higher the PCOs content is. However, the Procyanidolic Index is a value that can measure well over 100. Unfortunately, a Procyanidolic Index of 95 was erroneously taken to mean 95% PCO by some, all current methods of analysis suggest that the actual PCO content of these products is much lower than 95%. Gel permeation chromatography analysis allows separation of monomers from larger proanthocyanidin molecules, monomers of proanthocyanidins can be characterized by analysis with HPLC and mass spectrometry. Tandem mass spectrometry can be used to sequence proanthocyanidins, oligomeric proanthocyanidins strictly refer to dimer and trimer polymerizations of catechins
26.
Conformational isomerism
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In chemistry, conformational isomerism is a form of stereoisomerism in which the isomers can be interconverted exclusively by rotations about formally single bonds. Such isomers are generally referred to as conformational isomers or conformers and, specifically, rotations about single bonds are restricted by a rotational energy barrier which must be overcome to interconvert one conformer to another. Conformational isomerism arises when the rotation about a bond is relatively unhindered. That is, the barrier must be small enough for the interconversion to occur. Conformational isomers are thus distinct from the classes of stereoisomers where interconversion necessarily involves breaking and reforming of chemical bonds. The study of the energetics between different rotamers is referred to as conformational analysis and it is useful for understanding the stability of different isomers, for example, by taking into account the spatial orientation and through-space interactions of substituents. In addition, conformational analysis can be used to predict and explain product selectivity, mechanisms, the types of conformational isomers are related to the spatial orientations of the substituents between two vicinal atoms. The staggered conformation includes the gauche and anti conformations, depending on the orientations of the two substituents. The energy difference between gauche and anti is 0.9 kcal/mol associated with the energy of the gauche conformer. The anti conformer is, therefore, the most stable, the three eclipsed conformations with dihedral angles of 0°, 120°, and 240° are not considered to be rotamers, but are instead transition states of higher energy. While simple molecules can be described by these types of conformations, more specific examples of conformational isomerism are detailed elsewhere, Ring conformation Cyclohexane conformations with chair and boat conformers. Allylic strain – energetics related to rotation about the bond between sp2 and sp3 carbons. Atropisomerism – due to restricted rotation about a bond, a molecule can become chiral, folding of molecules, where some shapes are stable and functional, but others are not. Three isotherms are given in the depicting the equilibrium distribution of two conformers at different temperatures. At a free energy difference of 0 kcal/mol, this gives a constant of 1. The two have equal energy, neither is more stable, so neither predominates compared to the other. A negative difference in free energy means that a conformer interconverts to a more stable conformation. For example, the ΔG of butane from gauche to anti is −0.9 kcal/mol, therefore the equilibrium constant is 4.5, conversely, a positive difference in free energy means the conformer already is the more stable one, so the interconversion is an unfavorable equilibrium
27.
Laccase
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Laccases are copper-containing oxidase enzymes found in many plants, fungi, and microorganisms. Laccases act on phenols and similar molecules, performing one-electron oxidations and it is proposed that laccases play a role in the formation of lignin by promoting the oxidative coupling of monolignols, a family of naturally occurring phenols. Laccases can be polymeric, and the active form can be a dimer or trimer. Other laccases, such as produced by the fungus Pleurotus ostreatus, play a role in the degradation of lignin. Laccases require oxygen as a substrate for their enzymatic action. Spectrophotometry can be used to detect laccases, using the substrates ABTS, syringaldazine,2, 6-dimethoxyphenol, activity can also be monitored with an oxygen sensor, as the oxidation of the substrate is paired with the reduction of oxygen to water. Laccase was first studied by Gabriel Bertrand in 1894 in the sap of the Chinese lacquer tree, laccases can catalyze ring cleavage of aromatic compounds. The copper bound by laccase is bound in several sites, type 1, type 2, the ensemble of types 2 and 3 copper is called a trinuclear cluster. Type 1 copper is available to action of solvents, such as water and it can be displaced by mercury, substituted by cobalt or removed via a copper complexone. Removal of type 1 copper causes a decrease in laccase activity, cyanide can remove all copper from the enzyme, and re-embedding with type 1 and type 2 copper has been shown to be impossible. Type 3 copper, however, can be re-embedded back into the enzyme, Laccase can be inhibited by small ions such as, azide, halides, cyanide, and fluoride. These ions bind to type 2 and type 3 copper and disrupts electron transfer via copper centers, metal ions, fatty acids, hydroxyglycine, and kojic acid can also inhibit laccase by causing amino acid residue changes, conformational changes or copper chelation. Laccases have been examined as the cathode in enzymatic biofuel cells and they can be paired with an electron mediator to facilitate electron transfer to a solid electrode wire. Laccases are some of the few oxidoreductases commercialized as industrial catalysts, the enzymes can be used for textile dyeing/textile finishing, wine cork making, teeth whitening, and many other industrial, environmental, diagnostic, and synthetic uses. Laccases can be used in bioremediation, protein ligand docking can be used to predict the putative pollutants that can be degraded by laccase. Laccases have the potential to cross link food polymers such as proteins, in non starch polysaccharides, such as arabinoxylans, laccase catalyzes the oxidative gelation of feruloylated arabinoxylans by dimerization of their ferulic esters. These cross links have been found to greatly increased the maximum resistance, the resistance was increased due to the crosslinking of AX via ferulic acid and resulting in a strong AX and gluten network. Although laccase is known to cross link AX, under the microscope it was found that the laccase also acted on the flour proteins, Laccase is also able to oxidize peptide bound tyrosine, but very poorly
28.
ABTS
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In biochemistry,2, 2-azino-bis or ABTS is chemical compound used to observe the reaction kinetics of specific enzymes. A common use for it is in the enzyme-linked immunosorbent assay to detect for binding of molecules to each other and it is commonly used as a substrate with hydrogen peroxide for a peroxidase enzyme or alone with blue multicopper oxidase enzymes. Its use allows the reaction kinetics of peroxidases themselves to be followed, in this way it also can be used to indirectly follow the reaction kinetics of any hydrogen peroxide-producing enzyme, or to simply quantify the amount of hydrogen peroxide in a sample. Under these conditions, the groups are fully deprotonated and the mediator exists as a dianion. Its new absorbance maximum of 420 nm light can easily be followed with a spectrophotometer and it is sometimes used as part of a glucose estimating reagent when finding glucose concentrations of solutions such as blood serum. ABTS is also used by the food industry and agricultural researchers to measure the antioxidant capacities of foods. In this assay, ABTS is converted to its radical cation by addition of sodium persulfate and this radical cation is blue in color and absorbs light at 734 nm. The ABTS radical cation is reactive towards most antioxidants including phenolics, thiols, during this reaction, the blue ABTS radical cation is converted back to its colorless neutral form. The reaction may be monitored spectrophotometrically and this assay is often referred to as the Trolox equivalent antioxidant capacity assay. The reactivity of the various antioxidants tested are compared to that of Trolox, based on the special chemical properties of formed free radicals, ABTS assay has been used to determine the antioxidant capacity of food products. For example, polyphenol compounds, which widely exist in fruit, can quench free radicals inside human body, the antioxidant potency of plant extract or food product has been measured by ABTS assay. One example with detailed method is the antioxidant activity analysis of Hibiscus products
29.
Procyanidin A2
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Procyanidin A2 is a A type proanthocyanidin. It is found in avocado, chestnut, cranberry juice concentrate, lychee fruit pericarb, peanut skins, Cinchona cortex, cinnamon cortex, Urvillea ulmaceae, procyanidin B2 can be converted into procyanidin A2 by radical oxidation using 1, 1-diphenyl-2-picrylhydrazyl radicals under neutral conditions. Wen, LR, Wu, D, Jiang, YM, Prasad, KN, Lin, S, Jiang, GX, He, JR, Zhao, MM, Luo, W, Yang, identification of flavonoids in litchi leaf and evaluation of anticancer activities
30.
Infrared
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It extends from the nominal red edge of the visible spectrum at 700 nanometers, to 1000000 nm. Most of the radiation emitted by objects near room temperature is infrared. Like all EMR, IR carries radiant energy, and behaves both like a wave and like its quantum particle, the photon, slightly more than half of the total energy from the Sun was eventually found to arrive on Earth in the form of infrared. The balance between absorbed and emitted infrared radiation has an effect on Earths climate. Infrared radiation is emitted or absorbed by molecules when they change their rotational-vibrational movements and it excites vibrational modes in a molecule through a change in the dipole moment, making it a useful frequency range for study of these energy states for molecules of the proper symmetry. Infrared spectroscopy examines absorption and transmission of photons in the infrared range, Infrared radiation is used in industrial, scientific, and medical applications. Night-vision devices using active near-infrared illumination allow people or animals to be observed without the observer being detected, Infrared thermal-imaging cameras are used to detect heat loss in insulated systems, to observe changing blood flow in the skin, and to detect overheating of electrical apparatuses. Thermal-infrared imaging is used extensively for military and civilian purposes, military applications include target acquisition, surveillance, night vision, homing, and tracking. Humans at normal body temperature radiate chiefly at wavelengths around 10 μm, Infrared radiation extends from the nominal red edge of the visible spectrum at 700 nanometers to 1 mm. This range of wavelengths corresponds to a range of approximately 430 THz down to 300 GHz. Below infrared is the portion of the electromagnetic spectrum. Sunlight, at a temperature of 5,780 kelvins, is composed of near thermal-spectrum radiation that is slightly more than half infrared. At zenith, sunlight provides an irradiance of just over 1 kilowatt per square meter at sea level, of this energy,527 watts is infrared radiation,445 watts is visible light, and 32 watts is ultraviolet radiation. Nearly all the radiation in sunlight is near infrared, shorter than 4 micrometers. On the surface of Earth, at far lower temperatures than the surface of the Sun, almost all thermal radiation consists of infrared in mid-infrared region, much longer than in sunlight. Of these natural thermal radiation processes only lightning and natural fires are hot enough to produce much visible energy, thermal infrared radiation also has a maximum emission wavelength, which is inversely proportional to the absolute temperature of object, in accordance with Wiens displacement law. Therefore, the band is often subdivided into smaller sections. Due to the nature of the blackbody radiation curves, typical hot objects, such as exhaust pipes, the three regions are used for observation of different temperature ranges, and hence different environments in space
31.
Nuclear magnetic resonance spectroscopy
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Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy, is a research technique that exploits the magnetic properties of certain atomic nuclei. This type of spectroscopy determines the physical and chemical properties of atoms or the molecules in which they are contained and it relies on the phenomenon of nuclear magnetic resonance and can provide detailed information about the structure, dynamics, reaction state, and chemical environment of molecules. Suitable samples range from small compounds analyzed with 1-dimensional proton or carbon-13 NMR spectroscopy to large proteins or nucleic acids using 3 or 4-dimensional techniques. The impact of NMR spectroscopy on the sciences has been substantial because of the range of information, NMR spectra are unique, well-resolved, analytically tractable and often highly predictable for small molecules. Thus, in organic chemistry practice, NMR analysis is used to confirm the identity of a substance, different functional groups are obviously distinguishable, and identical functional groups with differing neighboring substituents still give distinguishable signals. NMR has largely replaced traditional wet chemistry tests such as reagents or typical chromatography for identification. A disadvantage is that a large amount, 2–50 mg, of a purified substance is required. Preferably, the sample should be dissolved in a solvent, because NMR analysis of solids requires a dedicated MAS machine, the timescale of NMR is relatively long, and thus it is not suitable for observing fast phenomena, producing only an averaged spectrum. NMR spectrometers are relatively expensive, universities usually have them, modern NMR spectrometers have a very strong, large and expensive liquid helium-cooled superconducting magnet, because resolution directly depends on magnetic field strength. There are even benchtop NMR spectrometers, the Purcell group at Harvard University and the Bloch group at Stanford University independently developed NMR spectroscopy in the late 1940s and early 1950s. Edward Mills Purcell and Felix Bloch shared the 1952 Nobel Prize in Physics for their discoveries, when placed in a magnetic field, NMR active nuclei absorb electromagnetic radiation at a frequency characteristic of the isotope. The resonant frequency, energy of the absorption, and the intensity of the signal are proportional to the strength of the magnetic field, for example, in a 21 Tesla magnetic field, protons resonate at 900 MHz. It is common to refer to a 21 T magnet as a 900 MHz magnet, spinning the sample is necessary to average out diffusional motion. Whereas, measurements of diffusion constants are done the sample stationary and spinning off, the vast majority of nuclei in a solution would belong to the solvent, and most regular solvents are hydrocarbons and would contain NMR-reactive protons. The most used deuterated solvent is deuterochloroform, although deuterium oxide and deuterated DMSO are used for hydrophilic analytes, the chemical shifts are slightly different in different solvents, depending on electronic solvation effects. NMR spectra are often calibrated against the known solvent residual proton peak instead of added tetramethylsilane, to detect the very small frequency shifts due to nuclear magnetic resonance, the applied magnetic field must be constant throughout the sample volume. High resolution NMR spectrometers use shims to adjust the homogeneity of the field to parts per billion in a volume of a few cubic centimeters. In order to detect and compensate for inhomogeneity and drift in the magnetic field, in modern NMR spectrometers shimming is adjusted automatically, though in some cases the operator has to optimize the shim parameters manually to obtain the best possible resolution
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