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.
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
6.
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
7.
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
8.
Boiling point
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The boiling point of a substance is the temperature at which the vapor pressure of the liquid equals the pressure surrounding the liquid and the liquid changes into a vapor. The boiling point of a liquid varies depending upon the environmental pressure. A liquid in a vacuum has a lower boiling point than when that liquid is at atmospheric pressure. A liquid at high pressure has a boiling point than when that liquid is at atmospheric pressure. For a given pressure, different liquids boil at different temperatures, for example, water boils at 100 °C at sea level, but at 93.4 °C at 2,000 metres altitude. The normal boiling point of a liquid is the case in which the vapor pressure of the liquid equals the defined atmospheric pressure at sea level,1 atmosphere. At that temperature, the pressure of the liquid becomes sufficient to overcome atmospheric pressure. The standard boiling point has been defined by IUPAC since 1982 as the temperature at which boiling occurs under a pressure of 1 bar, the heat of vaporization is the energy required to transform a given quantity of a substance from a liquid into a gas at a given pressure. Liquids may change to a vapor at temperatures below their boiling points through the process of evaporation, evaporation is a surface phenomenon in which molecules located near the liquids edge, not contained by enough liquid pressure on that side, escape into the surroundings as vapor. On the other hand, boiling is a process in which molecules anywhere in the liquid escape, a saturated liquid contains as much thermal energy as it can without boiling. The saturation temperature is the temperature for a corresponding saturation pressure at which a liquid boils into its vapor phase, the liquid can be said to be saturated with thermal energy. Any addition of energy results in a phase transition. If the pressure in a system remains constant, a vapor at saturation temperature will begin to condense into its liquid phase as thermal energy is removed, similarly, a liquid at saturation temperature and pressure will boil into its vapor phase as additional thermal energy is applied. The boiling point corresponds to the temperature at which the pressure of the liquid equals the surrounding environmental pressure. Thus, the point is dependent on the pressure. Boiling points may be published with respect to the NIST, USA standard pressure of 101.325 kPa, at higher elevations, where the atmospheric pressure is much lower, the boiling point is also lower. The boiling point increases with increased pressure up to the critical point, the boiling point cannot be increased beyond the critical point. Likewise, the point decreases with decreasing pressure until the triple point is reached
9.
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
10.
Irritation
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Irritation, in biology and physiology, is a state of inflammation or painful reaction to allergy or cell-lining damage. A stimulus or agent which induces the state of irritation is an irritant, irritants are typically thought of as chemical agents but mechanical, thermal, and radiative stimuli can also be irritants. Irritation also has non-clinical usages referring to physical or psychological pain or discomfort. Irritation can also be induced by some allergic response due to exposure of some allergens for example contact dermatitis, irritation of mucousal membranes, mucosal membrane is most common site of irritation because it contains secretory glands that release mucous which attracts the allergens due to its sticky nature. Chronic irritation is a term signifying that afflictive health conditions have been present for a while. There are many disorders that can cause irritation, the majority involves the skin, vagina, eyes. In higher organisms, a response may be the cause of irritation. It is a form of stress, but conversely, if one is stressed by unrelated matters, mild imperfections can cause more irritation than usual, one is irritable, see also sensitivity. In more basic organisms, the status of pain is the perception of the being stimulated and it is not proven that oysters can feel pain, but it is known that they react to irritants. When an irritating object becomes trapped within a shell, it deposits layers of calcium carbonate, slowly increasing in size. This is purely a defense mechanism, to trap a potentially threatening irritant such as a parasite inside its shell, or an attack from outside, the oyster creates a pearl sac to seal off the irritation. It has also observed that an amoeba avoids being prodded with a pin. Irritation is apparently the only universal sense shared by even single-celled creatures and it is postulated that most such beings also feel pain, but this is a projection – empathy. Modern office work with use of equipment has raised concerns about possible adverse health effects. Since the 1970s, reports have linked mucosal, skin, emission of various particulate and volatile substances has been suggested as specific causes. These symptoms have been related to Sick Building Syndrome, which involves symptoms such as irritation to the eyes, skin, the eye is also a source of chronic irritation. Disorders like Sjögrens syndrome, where one does not make tears, the condition is difficult to treat and is lifelong. Besides artificial tears, there is a drug called Restasis which may help, blepharitis is dryness and itching on the upper eyelids
11.
Toxic
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Toxicity is the degree to which a substance can damage an organism. Toxicity can refer to the effect on an organism, such as an animal, bacterium, or plant, as well as the effect on a substructure of the organism. By extension, the word may be used to describe toxic effects on larger and more complex groups. Sometimes the word is more or less synonymous with poisoning in everyday usage, toxicity is species-specific, making cross-species analysis problematic. Newer paradigms and metrics are evolving to bypass animal testing, while maintaining the concept of toxicity endpoints, disease-causing microorganisms and parasites are toxic in a broad sense, but are generally called pathogens rather than toxicants. The biological toxicity of pathogens can be difficult to measure because the dose may be a single organism. Theoretically one virus, bacterium or worm can reproduce to cause a serious infection, in some cases, e. g. cholera, the disease is chiefly caused by a nonliving substance secreted by the organism, rather than the organism itself. Such nonliving biological toxicants are generally called toxins if produced by a microorganism, plant, or fungus, Physical toxicants are substances that, due to their physical nature, interfere with biological processes. Examples include coal dust, asbestos fibers or finely divided silicon dioxide, corrosive chemicals possess physical toxicity because they destroy tissues, but theyre not directly poisonous unless they interfere directly with biological activity. Water can act as a physical toxicant if taken in high doses because the concentration of vital ions decreases dramatically if theres too much water in the body. Asphyxiant gases can be considered physical toxicants because they act by displacing oxygen in the environment but they are inert, as already mentioned, radiation can have a toxic effect on organisms. Toxicity can be measured by its effects on the target, one such measure is the LD50. When such data does not exist, estimates are made by comparison to known similar toxic things, then, safety factors are added to account for uncertainties in data and evaluation processes. Similarly, an extra protection factor may be used for individuals believed to be susceptible to toxic effects such as in pregnancy or with certain diseases. Obviously, this approach is approximate, but such protection factors are deliberately very conservative. In addition, it is possible that a single cell transformed into a cell is all it takes to develop the full effect. Common mixtures include gasoline, cigarette smoke, and industrial waste, even more complex are situations with more than one type of toxic entity, such as the discharge from a malfunctioning sewage treatment plant, with both chemical and biological agents. The preclinical toxicity testing on various biological systems reveals the species-, organ-, the toxicity of substances can be observed by studying the accidental exposures to a substance in vitro studies using cells/ cell lines in vivo exposure on experimental animals
12.
Organic compound
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An organic compound is virtually any chemical compound that contains carbon, although a consensus definition remains elusive and likely arbitrary. Organic compounds are rare terrestrially, but of importance because all known life is based on organic compounds. The most basic petrochemicals are considered the building blocks of organic chemistry, for historical reasons discussed below, a few types of carbon-containing compounds, such as carbides, carbonates, simple oxides of carbon, and cyanides are considered inorganic. The distinction between organic and inorganic compounds, while useful in organizing the vast subject of chemistry. Organic chemistry is the science concerned with all aspects of organic compounds, Organic synthesis is the methodology of their preparation. The word organic is historical, dating to the 1st century, for many centuries, Western alchemists believed in vitalism. This is the theory that certain compounds could be synthesized only from their classical elements—earth, water, air, vitalism taught that these organic compounds were fundamentally different from the inorganic compounds that could be obtained from the elements by chemical manipulation. Vitalism survived for a while even after the rise of modern atomic theory and it first came under question in 1824, when Friedrich Wöhler synthesized oxalic acid, a compound known to occur only in living organisms, from cyanogen. A more decisive experiment was Wöhlers 1828 synthesis of urea from the inorganic salts potassium cyanate, urea had long been considered an organic compound, as it was known to occur only in the urine of living organisms. Wöhlers experiments were followed by others, in which increasingly complex organic substances were produced from inorganic ones without the involvement of any living organism. Even though vitalism has been discredited, scientific nomenclature retains the distinction between organic and inorganic compounds, still, even the broadest definition requires excluding alloys that contain carbon, including steel. The C-H definition excludes compounds that are considered organic, neither urea nor oxalic acid is organic by this definition, yet they were two key compounds in the vitalism debate. The IUPAC Blue Book on organic nomenclature specifically mentions urea and oxalic acid, other compounds lacking C-H bonds but traditionally considered organic include benzenehexol, mesoxalic acid, and carbon tetrachloride. Mellitic acid, which contains no C-H bonds, is considered an organic substance in Martian soil. The C-H bond-only rule also leads to somewhat arbitrary divisions in sets of carbon-fluorine compounds, for example, CF4 would be considered by this rule to be inorganic, whereas CF3H would be organic. Organic compounds may be classified in a variety of ways, one major distinction is between natural and synthetic compounds. Another distinction, based on the size of organic compounds, distinguishes between small molecules and polymers, natural compounds refer to those that are produced by plants or animals. Many of these are extracted from natural sources because they would be more expensive to produce artificially
13.
Viscosity
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The viscosity of a fluid is a measure of its resistance to gradual deformation by shear stress or tensile stress. For liquids, it corresponds to the concept of thickness, for example. Viscosity is a property of the fluid which opposes the motion between the two surfaces of the fluid in a fluid that are moving at different velocities. For a given velocity pattern, the stress required is proportional to the fluids viscosity, a fluid that has no resistance to shear stress is known as an ideal or inviscid fluid. Zero viscosity is observed only at low temperatures in superfluids. Otherwise, all fluids have positive viscosity, and are said to be viscous or viscid. A fluid with a high viscosity, such as pitch. The word viscosity is derived from the Latin viscum, meaning mistletoe, the dynamic viscosity of a fluid expresses its resistance to shearing flows, where adjacent layers move parallel to each other with different speeds. It can be defined through the situation known as a Couette flow. This fluid has to be homogeneous in the layer and at different shear stresses, if the speed of the top plate is small enough, the fluid particles will move parallel to it, and their speed will vary linearly from zero at the bottom to u at the top. Each layer of fluid will move faster than the one just below it, in particular, the fluid will apply on the top plate a force in the direction opposite to its motion, and an equal but opposite one to the bottom plate. An external force is required in order to keep the top plate moving at constant speed. The magnitude F of this force is found to be proportional to the u and the area A of each plate. The proportionality factor μ in this formula is the viscosity of the fluid, the ratio u/y is called the rate of shear deformation or shear velocity, and is the derivative of the fluid speed in the direction perpendicular to the plates. Isaac Newton expressed the forces by the differential equation τ = μ ∂ u ∂ y, where τ = F/A. This formula assumes that the flow is moving along parallel lines and this equation can be used where the velocity does not vary linearly with y, such as in fluid flowing through a pipe. Use of the Greek letter mu for the dynamic viscosity is common among mechanical and chemical engineers. However, the Greek letter eta is used by chemists, physicists
14.
Liquid
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A liquid is a nearly incompressible fluid that conforms to the shape of its container but retains a constant volume independent of pressure. As such, it is one of the four states of matter. A liquid is made up of tiny vibrating particles of matter, such as atoms, water is, by far, the most common liquid on Earth. Like a gas, a liquid is able to flow and take the shape of a container, most liquids resist compression, although others can be compressed. Unlike a gas, a liquid does not disperse to fill every space of a container, a distinctive property of the liquid state is surface tension, leading to wetting phenomena. The density of a liquid is usually close to that of a solid, therefore, liquid and solid are both termed condensed matter. On the other hand, as liquids and gases share the ability to flow, although liquid water is abundant on Earth, this state of matter is actually the least common in the known universe, because liquids require a relatively narrow temperature/pressure range to exist. Most known matter in the universe is in form as interstellar clouds or in plasma form within stars. Liquid is one of the four states of matter, with the others being solid, gas. Unlike a solid, the molecules in a liquid have a greater freedom to move. The forces that bind the molecules together in a solid are only temporary in a liquid, a liquid, like a gas, displays the properties of a fluid. A liquid can flow, assume the shape of a container, if liquid is placed in a bag, it can be squeezed into any shape. These properties make a suitable for applications such as hydraulics. Liquid particles are bound firmly but not rigidly and they are able to move around one another freely, resulting in a limited degree of particle mobility. As the temperature increases, the vibrations of the molecules causes distances between the molecules to increase. When a liquid reaches its point, the cohesive forces that bind the molecules closely together break. If the temperature is decreased, the distances between the molecules become smaller, only two elements are liquid at standard conditions for temperature and pressure, mercury and bromine. Four more elements have melting points slightly above room temperature, francium, caesium, gallium and rubidium, metal alloys that are liquid at room temperature include NaK, a sodium-potassium metal alloy, galinstan, a fusible alloy liquid, and some amalgams
15.
Odor
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An odor or odour or fragrance is caused by one or more volatilized chemical compounds, generally at a very low concentration, that humans or other animals perceive by the sense of olfaction. Odors are also commonly called scents, which can refer to both pleasant and unpleasant odors, the terms fragrance and aroma are used primarily by the food and cosmetic industry to describe a pleasant odor, and are sometimes used to refer to perfumes, and to describe floral scent. In contrast, malodor, stench, reek, and stink are used specifically to describe unpleasant odor, the term smell is used for both pleasant and unpleasant odors. In the United Kingdom, odour refers to scents in general, the sense of smell gives rise to the perception of odors, mediated by the olfactory nerve. The olfactory receptor cells are present in the olfactory epithelium. There are millions of olfactory receptor neurons that act as sensory signaling cells, each neuron has cilia in direct contact with air. The olfactory nerve is considered the smell mediator, the axon connects the brain to the external air, odorous molecules act as a chemical stimulus. Molecules bind to receptor proteins extended from cilia, initiating an electric signal, thus, by using a chemical that binds to copper in the mouse nose, so that copper wasn’t available to the receptors, the authors showed that the mice couldnt detect the thiols. However, these also found that MOR244-3 lacks the specific metal ion binding site suggested by Suslick. When the signal reaches a threshold, the fires, sending a signal traveling along the axon to the olfactory bulb. Interpretation of the begins, relating the smell to past experiences. The olfactory bulb acts as a station connecting the nose to the olfactory cortex in the brain. Olfactory information is processed and projected through a pathway to the central nervous system. Odor sensation usually depends on the concentration available to the olfactory receptors, the olfactory system does not interpret a single compound, but instead the whole odorous mix, not necessarily corresponding to concentration or intensity of any single constituent. The widest range of odors consists of compounds, although some simple compounds not containing carbon, such as hydrogen sulfide. The perception of an effect is a two-step process. First, there is the part, the detection of stimuli by receptors in the nose. The stimuli are processed by the region of the brain which is responsible for olfaction
16.
Indole
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Indole is an aromatic heterocyclic organic compound with formula C8H7N. It has a structure, consisting of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring. Indole is widely distributed in the environment and can be produced by a variety of bacteria. As an intercellular signal molecule, indole regulates various aspects of physiology, including spore formation, plasmid stability, resistance to drugs, biofilm formation. The amino acid tryptophan is a derivative and the precursor of the neurotransmitter serotonin. Indole is a solid at room temperature, Indole can be produced by bacteria as a degradation product of the amino acid tryptophan. It occurs naturally in feces and has an intense fecal odor. At very low concentrations, however, it has a flowery smell and it also occurs in coal tar. The corresponding substituent is called indolyl, Indole undergoes electrophilic substitution, mainly at position 3. Substituted indoles are structural elements of the tryptophan-derived tryptamine alkaloids like the neurotransmitter serotonin, other indolic compounds include the plant hormone auxin, tryptophol, the anti-inflammatory drug indomethacin, the betablocker pindolol, and the naturally occurring hallucinogen dimethyltryptamine. The name indole is a portmanteau of the indigo and oleum. Indole chemistry began to develop with the study of the dye indigo, indigo can be converted to isatin and then to oxindole. Then, in 1866, Adolf von Baeyer reduced oxindole to indole using zinc dust, in 1869, he proposed a formula for indole. Certain indole derivatives were important dyestuffs until the end of the 19th century, in the 1930s, interest in indole intensified when it became known that the indole substituent is present in many important alkaloids, and it remains an active area of research today. It condenses with serine by Michael addition of indole to PLP-aminoacrylate, as an intercellular signal molecule, indole regulates various aspects of bacterial physiology, including spore formation, plasmid stability, resistance to drugs, biofilm formation, and virulence. The amino acid tryptophan is a derivative and the precursor of the neurotransmitter serotonin. Indole is a constituent of coal tar, and the 220–260 °C distillation fraction is the main industrial source of the material. Indole and its derivatives can also be synthesized by a variety of methods, the main industrial routes start from aniline via vapor-phase reaction with ethylene glycol in the presence of catalysts, In general, reactions are conducted between 200 and 500 °C
17.
Methyl group
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A methyl group is an alkyl derived from methane, containing one carbon atom bonded to three hydrogen atoms — CH3. In formulas, the group is often abbreviated Me, such hydrocarbon groups occur in many organic compounds. It is a stable group in most molecules. While the methyl group is part of a larger molecule. The anion has eight electrons, the radical seven and the cation six. All three forms are highly reactive and rarely observed, the methylium cation exists in the gas phase, but is otherwise not encountered. Some compounds are considered to be sources of the CH3+ cation, the methanide anion exists only in rarefied gas phase or under exotic conditions. It can be produced by electrical discharge in ketene at low pressure, such reagents are generally prepared from the methyl halides, M + CH3X → MCH3 where M is an alkali metal. The methyl radical has the formula CH3 and it exists in dilute gases, but in more concentrated form it readily dimerizes to ethane. It can be produced by decomposition of only certain compounds. The reactivity of a methyl group depends on the adjacent substituents, methyl groups can be quite unreactive. For example, in compounds, the methyl group resists attack by even the strongest acids. The oxidation of a group occurs widely in nature and industry. The oxidation products derived from methyl are CH2OH, CHO, for example, permanganate often converts a methyl group to a carboxyl group, e. g. the conversion of toluene to benzoic acid. Ultimately oxidation of methyl groups gives protons and carbon dioxide, as seen in combustion, demethylation is a common process, and reagents that undergo this reaction are called methylating agents. Common methylating agents are dimethyl sulfate, methyl iodide, and methyl triflate, methanogenesis, the source of natural gas, arises via a demethylation reaction. Certain methyl groups can be deprotonated, for example, the acidity of the methyl groups in acetone is about 1020 more acidic than methane. The resulting carbanions are key intermediates in many reactions in organic synthesis and biosynthesis, fatty acids are produced in this way
18.
Skatole
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Skatole or 3-methylindole is a mildly toxic white crystalline organic compound belonging to the indole family. It occurs naturally in feces and coal tar and has a strong fecal odor, in low concentrations, it has a flowery smell and is found in several flowers and essential oils, including those of orange blossoms, jasmine, and Ziziphus mauritiana. It is used as a fragrance and fixative in many perfumes and its name is derived from the Greek root skato- meaning dung. Skatole was discovered in 1877 by the German physician Ludwig Brieger, skatole is also used by U. S. military in its non-lethal weaponry, specifically, malodorants. Skatole can be found as a crystalline or fine powder solid. It is nitrogenous, and one of the rings is a pyrrole and it is soluble in alcohol and benzene, and it gives a violet color in potassium ferrocyanide and sulfuric acid. Skatole has a ring system that displays aromaticity. It is continuous, planar, and follows the 4n+2 rule because it has 10 π electrons and it can be synthesized through a Fischer indole synthesis, which was developed by Emil Fischer. Skatole has been shown to be an attractant to gravid mosquitoes in field and laboratory conditions. Because this compound is present in feces, it is found in combined sewage overflows as streams and lakes containing CSO water have untreated human, knowledge of this attractant makes CSO sites of particular interest when studying mosquito-borne diseases such as West Nile virus. Skatole has been shown to cause pulmonary edema in goats, sheep, rats and it appears to selectively target club cells, which are the major site of cytochrome P450 enzymes in the lungs. These enzymes convert skatole to an intermediate, 3-methyleneindolenine, which damages cells by forming protein adducts. Skatole is used as the material in the synthesis of atiprosin. Indole 1-Methylindole 2-Methylindole 5-Methylindole 7-Methylindole Cadaverine Whats that smell
19.
Heterocyclic compound
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A heterocyclic compound or ring structure is a cyclic compound that has atoms of at least two different elements as members of its ring. Heterocyclic chemistry is the branch of chemistry dealing with the synthesis, properties. Examples of heterocyclic compounds include all of the acids, the majority of drugs, most biomass. Although heterocyclic compounds may be inorganic, most contain at least one carbon, while atoms that are neither carbon nor hydrogen are normally referred to in organic chemistry as heteroatoms, this is usually in comparison to the all-carbon backbone. But this does not prevent a compound such as borazine from being labelled heterocyclic, IUPAC recommends the Hantzsch-Widman nomenclature for naming heterocyclic compounds. Heterocyclic compounds can be classified based on their electronic structure. The saturated heterocycles behave like the acyclic derivatives, thus, piperidine and tetrahydrofuran are conventional amines and ethers, with modified steric profiles. Therefore, the study of heterocyclic chemistry focuses especially on unsaturated derivatives, included are pyridine, thiophene, pyrrole, and furan. Another large class of heterocycles are fused to rings, which for pyridine, thiophene, pyrrole, and furan are quinoline, benzothiophene, indole. Fusion of two benzene rings gives rise to a large family of compounds, respectively the acridine, dibenzothiophene, carbazole. The unsaturated rings can be classified according to the participation of the heteroatom in the pi system, heterocycles with three atoms in the ring are more reactive because of ring strain. Those containing one heteroatom are, in general, stable and those with two heteroatoms are more likely to occur as reactive intermediates. Five-membered rings with one heteroatom, The 5-membered ring compounds containing two heteroatoms, at least one of which is nitrogen, are called the azoles. Thiazoles and isothiazoles contain a sulfur and an atom in the ring. A large group of 5-membered ring compounds with three heteroatoms also exists, one example is dithiazoles that contain two sulfur and a nitrogen atom. Five-member ring compounds with four heteroatoms, With 5-heteroatoms, the compound may be considered rather than heterocyclic. With 7-membered rings, the heteroatom must be able to provide an empty pi orbital for normal aromatic stabilization to be available, otherwise, for example, with the benzo-fused unsaturated nitrogen heterocycles, pyrrole provides indole or isoindole depending on the orientation. The pyridine analog is quinoline or isoquinoline, for azepine, benzazepine is the preferred name
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