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.
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
3.
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
4.
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
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.
Auxin
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Auxins are a class of plant hormones with some morphogen-like characteristics. Auxins have a role in coordination of many growth and behavioral processes in the plants life cycle and are essential for plant body development. Auxins and their role in plant growth were first described by the Dutch scientist Frits Warmolt Went, Kenneth V. Thimann was the first to isolate one of these phytohormones and determine its chemical structure as indole-3-acetic acid. Went and Thimann co-authored a book on plant hormones, Phytohormones, Auxins were the first of the major plant hormones to be discovered. They derive their name from the Greek word αυξειν, auxin is present in all parts of a plant, although in very different concentrations. The concentration in each position is crucial information, so it is subject to tight regulation through both metabolism and transport. The pattern of auxin distribution within the plant is a key factor for plant growth, its reaction to its environment and it is achieved through very complex and well coordinated active transport of auxin molecules from cell to cell throughout the plant body — by the so-called polar auxin transport. Thus, a plant can react to external conditions and adjust to them, Auxins typically act in concert with, or in opposition to, other plant hormones. For example, the ratio of auxin to cytokinin in certain plant tissues determines initiation of root versus shoot buds, on the molecular level, all auxins are compounds with an aromatic ring and a carboxylic acid group. The most important member of the family is indole-3-acetic acid, which generates the majority of auxin effects in intact plants. However, molecules of IAA are chemically labile in aqueous solution, five naturally occurring auxins in plants include indole-3-acetic acid, 4-chloroindole-3-acetic acid, phenylacetic acid, indole-3-butyric acid, and indole-3-propionic acid. Alongside endogenous auxins, scientists and manufacturers have developed many synthetic compounds with auxinic activity, synthetic auxin analogs include 1-naphthaleneacetic acid,2, 4-dichlorophenoxyacetic acid, and many others. Some synthetic auxins, such as 2, 4-D and 2,4, broad-leaf plants, such as dandelions, are much more susceptible to auxins than narrow-leaf plants such as grasses and cereal crops, so these synthetic auxins are valuable as synthetic herbicides. In 1881, Charles Darwin and his son Francis performed experiments on coleoptiles, the experiment exposed the coleoptile to light from a unidirectional source, and observed that they bend towards the light. By covering various parts of the coleoptiles with an opaque cap, the Darwins discovered that light is detected by the coleoptile tip. However the seedlings showed no signs of development towards light if the tip was covered with an opaque cap, in 1913, Danish scientist Peter Boysen-Jensen demonstrated that the signal was not transfixed but mobile. He separated the tip from the remainder of the coleoptile by a cube of gelatine which prevented cellular contact, the seedlings responded normally bending towards the light. However, when the tip was separated by an impermeable substance, in 1928, the Dutch botanist Frits Warmolt Went showed that a chemical messenger diffuses from coleoptile tips
9.
Rooting hormone
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Auxins are a class of plant hormones with some morphogen-like characteristics. Auxins have a role in coordination of many growth and behavioral processes in the plants life cycle and are essential for plant body development. Auxins and their role in plant growth were first described by the Dutch scientist Frits Warmolt Went, Kenneth V. Thimann was the first to isolate one of these phytohormones and determine its chemical structure as indole-3-acetic acid. Went and Thimann co-authored a book on plant hormones, Phytohormones, Auxins were the first of the major plant hormones to be discovered. They derive their name from the Greek word αυξειν, auxin is present in all parts of a plant, although in very different concentrations. The concentration in each position is crucial information, so it is subject to tight regulation through both metabolism and transport. The pattern of auxin distribution within the plant is a key factor for plant growth, its reaction to its environment and it is achieved through very complex and well coordinated active transport of auxin molecules from cell to cell throughout the plant body — by the so-called polar auxin transport. Thus, a plant can react to external conditions and adjust to them, Auxins typically act in concert with, or in opposition to, other plant hormones. For example, the ratio of auxin to cytokinin in certain plant tissues determines initiation of root versus shoot buds, on the molecular level, all auxins are compounds with an aromatic ring and a carboxylic acid group. The most important member of the family is indole-3-acetic acid, which generates the majority of auxin effects in intact plants. However, molecules of IAA are chemically labile in aqueous solution, five naturally occurring auxins in plants include indole-3-acetic acid, 4-chloroindole-3-acetic acid, phenylacetic acid, indole-3-butyric acid, and indole-3-propionic acid. Alongside endogenous auxins, scientists and manufacturers have developed many synthetic compounds with auxinic activity, synthetic auxin analogs include 1-naphthaleneacetic acid,2, 4-dichlorophenoxyacetic acid, and many others. Some synthetic auxins, such as 2, 4-D and 2,4, broad-leaf plants, such as dandelions, are much more susceptible to auxins than narrow-leaf plants such as grasses and cereal crops, so these synthetic auxins are valuable as synthetic herbicides. In 1881, Charles Darwin and his son Francis performed experiments on coleoptiles, the experiment exposed the coleoptile to light from a unidirectional source, and observed that they bend towards the light. By covering various parts of the coleoptiles with an opaque cap, the Darwins discovered that light is detected by the coleoptile tip. However the seedlings showed no signs of development towards light if the tip was covered with an opaque cap, in 1913, Danish scientist Peter Boysen-Jensen demonstrated that the signal was not transfixed but mobile. He separated the tip from the remainder of the coleoptile by a cube of gelatine which prevented cellular contact, the seedlings responded normally bending towards the light. However, when the tip was separated by an impermeable substance, in 1928, the Dutch botanist Frits Warmolt Went showed that a chemical messenger diffuses from coleoptile tips
10.
1-Naphthaleneacetic acid
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1-Naphthaleneacetic acid is an organic compound with the formula C10H7CH2CO2H. This colorless solid is soluble in organic solvents and it features a carboxylmethyl group linked to the 1-position of naphthalene. It is also used for plant tissue culture, the hormone NAA does not occur naturally, and, like all auxins, is toxic to plants at high concentrations. In the United States, under the Federal Insecticide, Fungicide, NAA is widely used in agriculture for various purposes. It is considered to be slightly toxic but when at higher concentrations it can be toxic to animals. This was shown when tested on rats via oral ingestion at 1000–5900 mg/kg, NAA has been shown to greatly increase cellulose fiber formation in plants when paired with another phytohormone called gibberellic acid. Because it is in the family it has also been understood to prevent premature dropping and thinning of fruits from stems. It is applied after blossom fertilization, increased amounts of it can actually have negative effects however, and cause growth inhibition to the development of plant crops. It has been used on different crops including apples, olives, oranges, potatoes. In order for it to obtain its desired effects it must be applied in concentrations ranging from 20-100 ug/mL, NAA present in the environment undergoes oxidation reactions with hydroxyl radicals and sulphate radicals. Radical reactions of NAA was studied by using pulse radiolysis technique, hydroxyl adduct radical was formed as the intermediate during the reaction of hydroxyl radical with NAA. The intermediate Naphtyl methyl radical was formed during the reaction of radical anion with NAA. In micro propagation of various plants NAA is typically added to a media containing nutrients essential to the plants survival and it is added to help induce root formation in various plant types. It can also be applied by spraying it on to plants and it is prohibited in many areas to use it in high concentrations due to the health concerns towards humans and other animals. NAA can be detected by HPLC-tandem mass spectrometry
11.
Plant hormone
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Plant hormones are chemicals that regulate plant growth. In the United Kingdom, these are termed plant growth substances, Plant hormones are signal molecules produced within the plant, and occur in extremely low concentrations. Hormones regulate cellular processes in targeted cells locally and, moved to other locations, hormones also determine the formation of flowers, stems, leaves, the shedding of leaves, and the development and ripening of fruit. Plants, unlike animals, lack glands that produce and secrete hormones, instead, each cell is capable of producing hormones. Plant hormones shape the plant, affecting seed growth, time of flowering, the sex of flowers, senescence of leaves, and fruits. They affect which tissues grow upward and which grow downward, leaf formation and stem growth, fruit development and ripening, plant longevity, hormones are vital to plant growth, and, lacking them, plants would be mostly a mass of undifferentiated cells. So they are known as growth factors or growth hormones. The term Phytohormone was coined by Thimann in 1948, the word hormone is derived from Greek, meaning set in motion. Plant hormones affect gene expression and transcription levels, cellular division and they are naturally produced within plants, though very similar chemicals are produced by fungi and bacteria that can also affect plant growth. A large number of related compounds are synthesized by humans. They are used to regulate the growth of cultivated plants, weeds, and in plants and plant cells. Early in the study of plant hormones, phytohormone was the commonly used term, Plant hormones are not nutrients, but chemicals that in small amounts promote and influence the growth, development, and differentiation of cells and tissues. The biosynthesis of plant hormones within plant tissues is often diffuse, plants utilize simple chemicals as hormones, which move more easily through their tissues. They are often produced and used on a basis within the plant body. Plant cells produce hormones that affect different regions of the cell producing the hormone. Hormones are transported within the plant by utilizing four types of movements, for localized movement, cytoplasmic streaming within cells and slow diffusion of ions and molecules between cells are utilized. Not all plant cells respond to hormones, but those cells that do are programmed to respond at specific points in their growth cycle, the greatest effects occur at specific stages during the cells life, with diminished effects occurring before or after this period. Plants need hormones at very specific times during plant growth and at specific locations and they also need to disengage the effects that hormones have when they are no longer needed
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
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