Jmol
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, or for research e.g. in chemistry and biochemistry. It is written in the programming language Java, so it can run on the operating systems Windows, macOS, 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 wide range of chemical file formats, including Protein Data Bank, Crystallographic Information File, MDL Molfile, Chemical Markup Language. There is 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, no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, the Sculpt mode. Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS 9. Jmol operates on a wide variety of platforms. For example, Jmol is functional in Mozilla Firefox, Internet Explorer, Google Chrome, Safari. Chemistry Development Kit Comparison of software for molecular mechanics modeling Jmol extension for MediaWiki List of molecular graphics systems Molecular graphics Molecule editor Proteopedia PyMOL SAMSON Official website Wiki with listings of websites and moodles Willighagen, Egon. "Fast and Scriptable Molecular Graphics in Web Browsers without Java3D". Doi:10.1038/npre.2007.50.1
Melting point
The melting point of a substance is the temperature at which it changes state from solid to liquid. At the melting point the solid and liquid phase exist in equilibrium; the melting point of a substance depends on pressure and is specified at a standard pressure such as 1 atmosphere or 100 kPa. When considered as the temperature of the reverse change from liquid to solid, it is referred to as the freezing point or crystallization point; because of the ability of some substances to supercool, the freezing point is not considered as a characteristic property of a substance. When the "characteristic freezing point" of a substance is determined, in fact the actual methodology is always "the principle of observing the disappearance rather than the formation of ice", that is, the melting point. For most substances and freezing points are 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. 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 not always the same as the melting point. In the absence of nucleators water can exist as a supercooled liquid down to −48.3 °C before freezing. The chemical element with the highest melting point is tungsten, at 3,414 °C; the often-cited carbon does not melt at ambient pressure but sublimes at about 3,726.85 °C. Tantalum hafnium carbide is a refractory compound with a high melting point of 4215 K. At the other end of the scale, helium does not freeze at all at normal pressure at temperatures arbitrarily close to absolute zero. 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 and a simple magnifier. The several grains of a solid are placed in a thin glass tube and immersed in the oil bath; the oil bath is heated and with the aid of the magnifier melting of the individual crystals at a certain temperature can be observed. In large/small devices, the sample is placed in a heating block, optical detection is automated; the measurement can be made continuously with an operating process. For instance, oil refineries measure the freeze point of diesel fuel online, meaning that the sample is taken from the process and measured automatically; this allows for more frequent measurements as the sample does not have to be manually collected and taken to a remote laboratory. For refractory materials the 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, 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; this extrapolation is accomplished by using Planck's law of radiation. The constants in this equation are not known with sufficient accuracy, causing errors in the extrapolation to become larger at higher temperatures. However, standard techniques have been developed to perform this extrapolation. Consider the case of using gold as the source. In this technique, the current through the filament of the pyrometer is adjusted until the light intensity of the filament matches that of a black-body at the melting point of gold.
This establishes the primary calibration temperature and can be expressed in terms of current through the pyrometer lamp. With the same current setting, the pyrometer is sighted on another black-body at a higher temperature. An absorbing medium of known transmission is inserted between this black-body; the temperature of the black-body is adjusted until a match exists between its intensity and that of the pyrometer filament. The true higher temperature of the black-body is determined from Planck's Law; the absorbing medium is removed and the current through the filament is adjusted to match the filament intensity to that of the black-body. This establishes a second calibration point for the pyrometer; this step is repeated to carry the calibration to hi
Hindered amine light stabilizers
Hindered amine light stabilizers are chemical compounds containing an amine functional group that are used as stabilizers in plastics and polymers. These compounds are derivatives of tetramethylpiperidine and are used to protect the polymers from the effects of photo-oxidation, they are increasingly being used as thermal stabilizers for low and moderate level of heat, however during the high temperature processing of polymers they remain less effective than traditional phenolic antioxidants. HALS do not absorb UV radiation, but act to inhibit degradation of the polymer by continuously and cyclically removing free radicals that are produced by photo-oxidation of the polymer; the overall process is sometimes referred to as the Denisov cycle, after Evguenii T. Denisov and is exceedingly complex. Broadly, HALS react with the initial polymer peroxy radical and alkyl polymer radicals formed by the reaction of the polymer and oxygen, preventing further radical oxidation. By these reactions HALS are oxidised to their corresponding aminoxyl radicals, however they are able to return to their initial amine form via a series of additional radical reactions.
HALS's high efficiency and longevity are due to this cyclic process wherein the HALS are regenerated rather than consumed during the stabilization process. The use of a hindered amine possessing no alpha-hydrogens is key, as this prevents the HALS being converted into a nitrone species; this could either react with any alkene groups in the polymer to give inactive species. Though HALS are effective in polyolefins and polyurethane, they are ineffective in polyvinyl chloride, it is thought that their ability to form nitroxyl radicals is disrupted due them being protonated by HCl released by dehydrohalogenation of PVC. Hindered amine light stabilizers Eversorb® Light Stabilizers Gas treating
Simplified molecular-input line-entry system
The simplified molecular-input line-entry system is a specification in the 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 been extended. In 2007, an open standard called. Other linear notations include the Wiswesser line notation, ROSDAL, SYBYL Line Notation; the original SMILES specification was initiated by David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s. Acknowledged for their parts in the early development were "Gilman Veith and Rose Russo and Albert Leo and Corwin Hansch for supporting the work, Arthur Weininger and Jeremy Scofield for assistance in programming the system." The Environmental Protection Agency funded the initial project to develop SMILES. It has since been modified and extended by others, most notably by Daylight Chemical Information Systems.
In 2007, an open 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 considered to have the advantage of being more human-readable than InChI; the term SMILES refers to a line notation for encoding molecular structures and specific instances should be called SMILES strings. However, the term SMILES is commonly used to refer to both a single SMILES string and a number of SMILES strings; the terms "canonical" and "isomeric" can lead to some confusion when applied to SMILES. The terms are not mutually exclusive. A number of 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; this SMILES is unique for each structure, although dependent on the canonicalization algorithm used to generate it, is termed the canonical SMILES.
These algorithms first convert the SMILES to an internal representation of the molecular structure. Various algorithms for generating canonical SMILES have been developed and include those by Daylight Chemical Information Systems, OpenEye Scientific Software, MEDIT, Chemical Computing Group, MolSoft LLC, the Chemistry Development Kit. A common application of canonical SMILES is indexing and ensuring uniqueness of molecules in a database; the original paper that described the CANGEN algorithm claimed to generate unique SMILES strings for graphs representing molecules, but the algorithm fails for a number of simple cases and cannot be considered a correct method for representing a graph canonically. There is 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, double bond geometry; these are structural features that cannot be specified by connectivity alone and SMILES which encode this information are termed isomeric SMILES.
A notable feature of these rules is. The term isomeric SMILES is applied to SMILES in which isotopes are specified. In terms of a graph-based computational procedure, SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph; the chemical graph is first trimmed to remove hydrogen atoms and cycles are broken to turn it into a spanning tree. Where cycles have been broken, numeric suffix labels are included to indicate the connected nodes. Parentheses are used to indicate points of branching on the tree; the resultant SMILES form depends on the choices: of the bonds chosen to break cycles, of the starting atom used for the depth-first traversal, of the order in which branches are listed when encountered. Atoms are represented by the standard abbreviation of the chemical elements, in square brackets, such as for gold. Brackets may be omitted in the common case of atoms which: are in the "organic subset" of B, C, N, O, P, S, F, Cl, Br, or I, have no formal charge, have the number of hydrogens attached implied by the SMILES valence model, are the normal isotopes, are not chiral centers.
All other elements must be enclosed in brackets, have charges and hydrogens shown explicitly. For instance, the SMILES for water may be written as either O or. Hydrogen may be written as a separate atom; when brackets are used, the symbol H is added if the atom in brackets is bonded to one or more hydrogen, followed by the number of hydrogen atoms if greater than 1 by the sign + for a positive charge or by - for a negative charge. For example, for ammonium. If there is more than one charge, it is written as digit.
European Chemicals Agency
The European Chemicals Agency is an agency of the European Union which manages the technical and administrative aspects of the implementation of the European Union regulation called Registration, Evaluation and Restriction of Chemicals. ECHA is the driving force among regulatory authorities in implementing the EU's chemicals legislation. ECHA helps companies to comply with the legislation, advances the safe use of chemicals, provides information on chemicals and addresses chemicals of concern, it is located in Finland. The agency headed by Executive Director Bjorn Hansen, started working on 1 June 2007; the REACH Regulation requires companies to provide information on the hazards 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 used substances have been registered; the information is technical but gives detail on the impact of each chemical on people and the environment.
This gives European consumers the right to ask retailers whether the goods they buy contain dangerous substances. The Classification 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 and how to use products safely because the labels on products are now the same throughout the world. Companies need to notify ECHA of the labelling of their chemicals. So far, ECHA has received over 5 million notifications for more than 100 000 substances; the information is available on their website. Consumers can check chemicals in the products. Biocidal products include, for example, insect disinfectants used in hospitals; the Biocidal Products Regulation ensures that there is enough 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 import of hazardous chemicals.
Through this mechanism, countries due to receive hazardous chemicals are informed in advance and have the possibility of rejecting their import. Substances that may have serious effects on human health and the environment are identified as Substances of Very High Concern 1; these are substances which cause cancer, mutation or are toxic to reproduction as well as substances which persist in the body or the environment and do not break down. Other substances considered. Companies manufacturing or importing articles containing these substances in a concentration above 0,1% weight of the article, have legal obligations, 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 identified in the EU as being of 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 move to another list. This means that, after a given date, companies will not be allowed to place the substance on the market or to use it, unless they have been given prior authorisation to do so by ECHA. One of the main aims of this listing process is to phase out SVHCs where possible. In its 2018 substance evaluation progress report, ECHA said chemical companies failed to provide “important safety information” in nearly three quarters of cases checked that year. "The numbers show a similar picture to previous years" the report said. The agency noted that member states need to develop risk management measures to control unsafe commercial use of chemicals in 71% of the substances checked. Executive Director Bjorn Hansen called non-compliance with REACH a "worry". Industry group CEFIC acknowledged the problem; the European Environmental Bureau called for faster enforcement to minimise chemical exposure. European Chemicals Bureau Official website
Radical (chemistry)
In chemistry, a radical is an atom, molecule, or ion that has an unpaired valence electron. With some exceptions, these unpaired electrons make radicals chemically reactive. Many radicals spontaneously dimerize. Most organic radicals have short lifetimes. A notable example of a radical is the hydroxyl radical, a molecule that has one unpaired electron on the oxygen atom. Two other examples are triplet triplet carbene which have two unpaired electrons. Radicals may be generated in a number of ways. Ionizing radiation, electrical discharges, electrolysis are known to produce radicals. Radicals are intermediates in many chemical reactions, more so than is apparent from the balanced equations. Radicals are important in combustion, atmospheric chemistry, plasma chemistry and many other chemical processes. A large fraction of natural products is generated by radical-generating enzymes. In living organisms, the radicals superoxide and nitric oxide and their reaction products regulate many processes, such as control of vascular tone and thus blood pressure.
They play a key role in the intermediary metabolism of various biological compounds. Such radicals can be messengers in a process dubbed redox signaling. A radical may be otherwise bound. In chemical equations, radicals are denoted by a dot placed to the right of the atomic symbol or molecular formula as follows: C l 2 → U V 2 C l ⋅ Radical reaction mechanisms use single-headed arrows to depict the movement of single electrons: The homolytic cleavage of the breaking bond is drawn with a'fish-hook' arrow to distinguish from the usual movement of two electrons depicted by a standard curly arrow; the second electron of the breaking bond moves to pair up with the attacking radical electron. Radicals take part in radical addition and radical substitution as reactive intermediates. Chain reactions involving radicals can be divided into three distinct processes; these are initiation and termination. Initiation reactions are those, they may involve the formation of radicals from stable species as in Reaction 1 above or they may involve reactions of radicals with stable species to form more radicals.
Propagation reactions are those reactions involving radicals in which the total number of radicals remains the same. Termination reactions are those reactions resulting in a net decrease in the number of radicals. Two radicals combine to form a more stable species, for example: 2Cl·→ Cl2 Radicals can form by breaking of covalent bonds by homolysis; the homolytic bond dissociation energies abbreviated as "ΔH °" are a measure of bond strength. Splitting H2 into 2H•, for example, requires a ΔH ° of +435 kJ·mol-1, while splitting Cl2 into 2Cl• requires a ΔH ° of +243 kJ·mol-1. For weak bonds, homolysis can be induced thermally. Strong bonds require high energy photons or flames to induce homolysis. Radicals or charged species add to non-radicals to give new radicals; this process is the basis of the radical chain reaction. Being prevalent and a diradical, O2 reacts with many organic compounds to generate radicals together with the hydroperoxide radical; this process is related to rancidification of unsaturated fats.
Radicals may be formed by single-electron oxidation or reduction of an atom or molecule. These redox reactions occur in electrochemical cells and in ionization chambers of mass spectrometers. Although radicals are short-lived due to their reactivity, there are long-lived radicals; these are categorized as follows: The prime example of a stable radical is molecular dioxygen. Another common example is nitric oxide. Organic radicals can be long lived if they occur in a conjugated π system, such as the radical derived from α-tocopherol. There are hundreds of examples of thiazyl radicals, which show low reactivity and remarkable thermodynamic stability with only a limited extent of π resonance stabilization. Persistent radical compounds are those whose longevity is due to steric crowding around the radical center, which makes it physically difficult for the radical to react with another molecule. Examples of these include Gomberg's triphenylmethyl radical, Fremy's salt, such as TEMPO, TEMPOL, nitronyl nitroxides, azephenylenyls and radicals derived from PTM and TTM.
Persistent radicals are generated in great quantity during combustion, "may be responsible for the oxidative stress resulting in cardiopulmonary disease and cancer, attributed to exposure to airborne fine particles". Gomberg's free radical can be generated by following reaction in lab - 3C-Cl + Ag === 3C• + AgCl The reason for persistivity of free radicals is either the delocalisation of unpaired electron or the unavailability of unpaired electron to other species due to the screening of neighbouring atoms/groups. Diradicals are molecules containing two radical centers. Multiple radical centers can exist in a molecule. Atmospheric oxygen exists as a diradical in its ground state as triplet oxygen; the low reactivity of atmospheric oxygen is due to its diradical state. Non-radical states of dioxygen are less stable tha
Catalysis
Catalysis is the process of increasing the rate of a chemical reaction by adding a substance known as a catalyst, not consumed in the catalyzed reaction and can continue to act repeatedly. Because of this, only small amounts of catalyst are required to alter the reaction rate in principle. In general, chemical reactions occur faster in the presence of a catalyst because the catalyst provides an alternative reaction pathway with a lower activation energy than the non-catalyzed mechanism. In catalyzed mechanisms, the catalyst reacts to form a temporary intermediate, which regenerates the original catalyst in a cyclic process. A substance which provides a mechanism with a higher activation energy does not decrease the rate because the reaction can still occur by the non-catalyzed route. An added substance which does reduce the reaction rate is not considered a catalyst but a reaction inhibitor. Catalysts may be classified as either heterogeneous. A homogeneous catalyst is one whose molecules are dispersed in the same phase as the reactant's molecules.
A heterogeneous catalyst is one whose molecules are not in the same phase as the reactant's, which are gases or liquids that are adsorbed onto the surface of the solid catalyst. Enzymes and other biocatalysts are considered as a third category. In the presence of a catalyst, less free energy is required to reach the transition state, but the total free energy from reactants to products does not change. A catalyst may participate in multiple chemical transformations; the effect of a catalyst may vary due to the presence of other substances known as inhibitors or poisons or promoters. Catalyzed reactions have a lower activation energy than the corresponding uncatalyzed reaction, resulting in a higher reaction rate at the same temperature and for the same reactant concentrations. However, the detailed mechanics of catalysis is complex. Catalysts may bind to the reagents to polarize bonds, e.g. acid catalysts for reactions of carbonyl compounds, or form specific intermediates that are not produced such as osmate esters in osmium tetroxide-catalyzed dihydroxylation of alkenes, or cause dissociation of reagents to reactive forms, such as chemisorbed hydrogen in catalytic hydrogenation.
Kinetically, catalytic reactions are typical chemical reactions. The catalyst participates in this slowest step, rates are limited by amount of catalyst and its "activity". In heterogeneous catalysis, the diffusion of reagents to the surface and diffusion of products from the surface can be rate determining. A nanomaterial-based catalyst is an example of a heterogeneous catalyst. Analogous events associated with substrate binding and product dissociation apply to homogeneous catalysts. Although catalysts are not consumed by the reaction itself, they may be inhibited, deactivated, or destroyed by secondary processes. In heterogeneous catalysis, typical secondary processes include coking where the catalyst becomes covered by polymeric side products. Additionally, heterogeneous catalysts can dissolve into the solution in a solid–liquid system or sublimate in a solid–gas system; the production of most industrially important chemicals involves catalysis. Most biochemically significant processes are catalysed.
Research into catalysis is a major field in applied science and involves many areas of chemistry, notably organometallic chemistry and materials science. Catalysis is relevant to many aspects of environmental science, e.g. the catalytic converter in automobiles and the dynamics of the ozone hole. Catalytic reactions are preferred in environmentally friendly green chemistry due to the reduced amount of waste generated, as opposed to stoichiometric reactions in which all reactants are consumed and more side products are formed. Many transition metals and transition metal complexes are used in catalysis as well. Catalysts called. A catalyst works by providing an alternative reaction pathway to the reaction product; the rate of the reaction is increased as this alternative route has a lower activation energy than the reaction route not mediated by the catalyst. The disproportionation of hydrogen peroxide creates oxygen, as shown below. 2 H2O2 → 2 H2O + O2This reaction is preferable in the sense that the reaction products are more stable than the starting material, though the uncatalysed reaction is slow.
In fact, the decomposition of hydrogen peroxide is so slow that hydrogen peroxide solutions are commercially available. This reaction is affected by catalysts such as manganese dioxide, or the enzyme peroxidase in organisms. Upon the addition of a small amount of manganese dioxide, the hydrogen peroxide reacts rapidly; this effect is seen by the effervescence of oxygen. The manganese dioxide is not consumed in the reaction, thus may be recovered unchanged, re-used indefinitely. Accordingly, manganese dioxide catalyses this reaction. Catalytic activity is denoted by the symbol z and measured in mol/s, a unit, called katal and defined the SI unit for catalytic activity since 1999. Catalytic activity is not a kind of reaction rate, but a property of the catalyst under certain conditions, in relation to a specific chemical reaction. Catalytic activity of one katal of a catalyst means one mole of that catalyst will catalyse 1 mole of the reactant to product in one second. A catalyst may and will have different catalytic activity for di
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