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.
In optics, the refractive index or index of refraction of a material is a dimensionless number that describes how fast light propagates through the material. It is defined as n = c v, where c is the speed of light in vacuum and v is the phase velocity of light in the medium. For example, the refractive index of water is 1.333, meaning that light travels 1.333 times as fast in vacuum as in water. The refractive index determines how much the path of light is bent, or refracted, when entering a material; this is described by Snell's law of refraction, n1 sinθ1 = n2 sinθ2, where θ1 and θ2 are the angles of incidence and refraction of a ray crossing the interface between two media with refractive indices n1 and n2. The refractive indices determine the amount of light, reflected when reaching the interface, as well as the critical angle for total internal reflection and Brewster's angle; the refractive index can be seen as the factor by which the speed and the wavelength of the radiation are reduced with respect to their vacuum values: the speed of light in a medium is v = c/n, the wavelength in that medium is λ = λ0/n, where λ0 is the wavelength of that light in vacuum.
This implies that vacuum has a refractive index of 1, that the frequency of the wave is not affected by the refractive index. As a result, the energy of the photon, therefore the perceived color of the refracted light to a human eye which depends on photon energy, is not affected by the refraction or the refractive index of the medium. While the refractive index affects wavelength, it depends on photon frequency and energy so the resulting difference in the bending angle causes white light to split into its constituent colors; this is called dispersion. It can be observed in prisms and rainbows, chromatic aberration in lenses. Light propagation in absorbing materials can be described using a complex-valued refractive index; the imaginary part handles the attenuation, while the real part accounts for refraction. The concept of refractive index applies within the full electromagnetic spectrum, from X-rays to radio waves, it can be applied to wave phenomena such as sound. In this case the speed of sound is used instead of that of light, a reference medium other than vacuum must be chosen.
The refractive index n of an optical medium is defined as the ratio of the speed of light in vacuum, c = 299792458 m/s, the phase velocity v of light in the medium, n = c v. The phase velocity is the speed at which the crests or the phase of the wave moves, which may be different from the group velocity, the speed at which the pulse of light or the envelope of the wave moves; the definition above is sometimes referred to as the absolute refractive index or the absolute index of refraction to distinguish it from definitions where the speed of light in other reference media than vacuum is used. Air at a standardized pressure and temperature has been common as a reference medium. Thomas Young was the person who first used, invented, the name "index of refraction", in 1807. At the same time he changed this value of refractive power into a single number, instead of the traditional ratio of two numbers; the ratio had the disadvantage of different appearances. Newton, who called it the "proportion of the sines of incidence and refraction", wrote it as a ratio of two numbers, like "529 to 396".
Hauksbee, who called it the "ratio of refraction", wrote it as a ratio with a fixed numerator, like "10000 to 7451.9". Hutton wrote it as a ratio with a fixed denominator, like 1.3358 to 1. Young did not use a symbol for the index of refraction, in 1807. In the next years, others started using different symbols: n, m, µ; the symbol n prevailed. For visible light most transparent media have refractive indices between 1 and 2. A few examples are given in the adjacent table; these values are measured at the yellow doublet D-line of sodium, with a wavelength of 589 nanometers, as is conventionally done. Gases at atmospheric pressure have refractive indices close to 1 because of their low density. All solids and liquids have refractive indices above 1.3, with aerogel as the clear exception. Aerogel is a low density solid that can be produced with refractive index in the range from 1.002 to 1.265. Moissanite lies at the other end of the range with a refractive index as high as 2.65. Most plastics have refractive indices in the range from 1.3 to 1.7, but some high-refractive-index polymers can have values as high as 1.76.
For infrared light refractive indices can be higher. Germanium is transparent in the wavelength region from 2 to 14 µm and has a refractive index of about 4. A type of new materials, called topological insulator, was found holding higher refractive index of up to 6 in near to mid infrared frequency range. Moreover, topological insulator material are transparent; these excellent properties make them a type of significant materials for infrared optics. According to the theory of relativity, no information can travel faster than the speed of light in vacuum, but this does not mean that the refractive index cannot be lower than 1; the refractive index measures the phase velocity of light. The phase velocity is the speed at which the crests of the wave move and can be faster than the speed of light in vacuum, thereby give a refractive index below 1; this can occur close to resonance frequencies, for absorbing media, in plasmas, for X-rays. In the X-ray regime the refractive indices are
Ethers are a class of organic compounds that contain an ether group—an oxygen atom connected to two alkyl or aryl groups. They have the general formula R -- O -- R ′, where R ′ represent the alkyl or aryl groups. Ethers can again be classified into two varieties: if the alkyl groups are the same on both sides of the oxygen atom it is a simple or symmetrical ether, whereas if they are different, the ethers are called mixed or unsymmetrical ethers. A typical example of the first group is the solvent and anesthetic diethyl ether referred to as "ether". Ethers are common in organic chemistry and more prevalent in biochemistry, as they are common linkages in carbohydrates and lignin. Ethers feature C–O–C linkage defined by a bond angle of about 110° and C–O distances of about 140 pm; the barrier to rotation about the C–O bonds is low. The bonding of oxygen in ethers and water is similar. In the language of valence bond theory, the hybridization at oxygen is sp3. Oxygen is more electronegative than carbon, thus the hydrogens alpha to ethers are more acidic than in simple hydrocarbons.
They are far less acidic than hydrogens alpha to carbonyl groups, however. Depending on the groups at R and R′, ethers are classified into two types:Simple ethers or symmetrical ethers. Mixed ethers or asymmetrical ethers. In the IUPAC nomenclature system, ethers are named using the general formula "alkoxyalkane", for example CH3–CH2–O–CH3 is methoxyethane. If the ether is part of a more-complex molecule, it is described as an alkoxy substituent, so –OCH3 would be considered a "methoxy-" group; the simpler alkyl radical is written in front, so CH3–O–CH2CH3 would be given as methoxyethane. IUPAC rules are not followed for simple ethers; the trivial names for simple ethers are a composite of the two substituents followed by "ether". For example, ethyl methyl ether, diphenylether; as for other organic compounds common ethers acquired names before rules for nomenclature were formalized. Diethyl ether is called "ether", but was once called sweet oil of vitriol. Methyl phenyl ether is anisole, because it was found in aniseed.
The aromatic ethers include furans. Acetals are another class of ethers with characteristic properties. Polyethers are compounds with more than one ether group; the crown ethers are examples of small polyethers. Some toxins produced by dinoflagellates such as brevetoxin and ciguatoxin are large and are known as cyclic or ladder polyethers. Polyether refers to polymers which contain the ether functional group in their main chain; the term glycol is reserved for low to medium range molar mass polymer when the nature of the end-group, a hydroxyl group, still matters. The term "oxide" or other terms are used for high molar mass polymer when end-groups no longer affect polymer properties; the phenyl ether polymers are a class of aromatic polyethers containing aromatic cycles in their main chain: Polyphenyl ether and Poly. Many classes of compounds with C–O–C linkages are not considered ethers: Esters, carboxylic acid anhydrides. Ether molecules cannot form hydrogen bonds with each other, resulting in low boiling points compared to those of the analogous alcohols.
The difference in the boiling points of the ethers and their isomeric alcohols becomes lower as the carbon chains become longer, as the van der Waals interactions of the extended carbon chain dominates over the presence of hydrogen bonding. Ethers are polar; the C–O–C bond angle in the functional group is about 110°, the C–O dipoles do not cancel out. Ethers are more polar than alkenes but not as polar as alcohols, esters, or amides of comparable structure; the presence of two lone pairs of electrons on the oxygen atoms makes hydrogen bonding with water molecules possible. Cyclic ethers such as tetrahydrofuran and 1,4-dioxane are miscible in water because of the more exposed oxygen atom for hydrogen bonding as compared to linear aliphatic ethers. Other properties are: The lower ethers are volatile and flammable. Lower ethers act as anaesthetics. Ethers are good organic solvents. Simple ethers are tasteless. Ethers are quite stable chemical compounds which do not react with bases, active metals, dilute acids, oxidising agents, reducing agents.
They are of low chemical reactivity, but they are more reactive than alkanes. Epoxides and acetals are unrepresentative classes of ethers and are discussed in separate articles. Important reactions are listed below. Although ethers resist hydrolysis, their polar bonds are cloven by mineral acids such as hydrobromic acid and hydroiodic acid. Hydrogen chloride cleaves ethers only slowly. Methyl ethers afford methyl halides: ROCH3 + HBr → CH3Br + ROHThese reactions proceed via onium intermediates, i.e. +Br−. Some ethers undergo rapid cleavage with boron tribromide to give the alkyl bromide. Depending on the substituents, some ethers can be cloven with a variety of reagents, e.g. strong base. When stored in the presence of air or oxygen, ethers tend to form explosive peroxides, such as diethyl ether peroxide; the reaction is accelerated by light, metal catalysts, aldehydes. In addition to avoiding storage conditions to form peroxides, it is recommended, when an ether is used as a solvent, not to distill it to dryness, as any peroxides that may have formed, being less volatil
The density, or more the volumetric mass density, of a substance is its mass per unit volume. The symbol most used for density is ρ, although the Latin letter D can be used. Mathematically, density is defined as mass divided by volume: ρ = m V where ρ is the density, m is the mass, V is the volume. In some cases, density is loosely defined as its weight per unit volume, although this is scientifically inaccurate – this quantity is more called specific weight. For a pure substance the density has the same numerical value as its mass concentration. Different materials have different densities, density may be relevant to buoyancy and packaging. Osmium and iridium are the densest known elements at standard conditions for temperature and pressure but certain chemical compounds may be denser. To simplify comparisons of density across different systems of units, it is sometimes replaced by the dimensionless quantity "relative density" or "specific gravity", i.e. the ratio of the density of the material to that of a standard material water.
Thus a relative density less than one means. The density of a material varies with pressure; this variation is small for solids and liquids but much greater for gases. Increasing the pressure on an object decreases the volume of the object and thus increases its density. Increasing the temperature of a substance decreases its density by increasing its volume. In most materials, heating the bottom of a fluid results in convection of the heat from the bottom to the top, due to the decrease in the density of the heated fluid; this causes it to rise relative to more dense unheated material. The reciprocal of the density of a substance is called its specific volume, a term sometimes used in thermodynamics. Density is an intensive property in that increasing the amount of a substance does not increase its density. In a well-known but apocryphal tale, Archimedes was given the task of determining whether King Hiero's goldsmith was embezzling gold during the manufacture of a golden wreath dedicated to the gods and replacing it with another, cheaper alloy.
Archimedes knew that the irregularly shaped wreath could be crushed into a cube whose volume could be calculated and compared with the mass. Baffled, Archimedes is said to have taken an immersion bath and observed from the rise of the water upon entering that he could calculate the volume of the gold wreath through the displacement of the water. Upon this discovery, he leapt from his bath and ran naked through the streets shouting, "Eureka! Eureka!". As a result, the term "eureka" entered common parlance and is used today to indicate a moment of enlightenment; the story first appeared in written form in Vitruvius' books of architecture, two centuries after it took place. Some scholars have doubted the accuracy of this tale, saying among other things that the method would have required precise measurements that would have been difficult to make at the time. From the equation for density, mass density has units of mass divided by volume; as there are many units of mass and volume covering many different magnitudes there are a large number of units for mass density in use.
The SI unit of kilogram per cubic metre and the cgs unit of gram per cubic centimetre are the most used units for density. One g/cm3 is equal to one thousand kg/m3. One cubic centimetre is equal to one millilitre. In industry, other larger or smaller units of mass and or volume are more practical and US customary units may be used. See below for a list of some of the most common units of density. A number of techniques as well as standards exist for the measurement of density of materials; such techniques include the use of a hydrometer, Hydrostatic balance, immersed body method, air comparison pycnometer, oscillating densitometer, as well as pour and tap. However, each individual method or technique measures different types of density, therefore it is necessary to have an understanding of the type of density being measured as well as the type of material in question; the density at all points of a homogeneous object equals its total mass divided by its total volume. The mass is measured with a scale or balance.
To determine the density of a liquid or a gas, a hydrometer, a dasymeter or a Coriolis flow meter may be used, respectively. Hydrostatic weighing uses the displacement of water due to a submerged object to determine the density of the object. If the body is not homogeneous its density varies between different regions of the object. In that case the density around any given location is determined by calculating the density of a small volume around that location. In the limit of an infinitesimal volume the density of an inhomogeneous object at a point becomes: ρ = d m / d V, where d V is an elementary volume at position r; the mass of the body t
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
Safety data sheet
A safety data sheet, material safety data sheet, or product safety data sheet is a document that lists information relating to occupational safety and health for the use of various substances and products. SDSs are a used system for cataloging information on chemicals, chemical compounds, chemical mixtures. SDS information may include instructions for the safe use and potential hazards associated with a particular material or product, along with spill-handling procedures. SDS formats can vary from source to source within a country depending on national requirements. A SDS for a substance is not intended for use by the general consumer, focusing instead on the hazards of working with the material in an occupational setting. There is a duty to properly label substances on the basis of physico-chemical, health or environmental risk. Labels can include hazard symbols such as the European Union standard symbols; the same product can have different formulations in different countries. The formulation and hazard of a product using a generic name may vary between manufacturers in the same country.
The Globally Harmonized System of Classification and Labelling of Chemicals contains a standard specification for safety data sheets. The SDS follows a 16 section format, internationally agreed and for substances the SDS should be followed with an Annex which contains the exposure scenarios of this particular substance; the 16 sections are: SECTION 1: Identification of the substance/mixture and of the company/undertaking 1.1. Product identifier 1.2. 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 SECTION 2: Hazards identification 2.1. Classification of the substance or mixture 2.2. Label elements 2.3. Other hazards SECTION 3: Composition/information on ingredients 3.1. Substances 3.2. Mixtures SECTION 4: 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 SECTION 5: Firefighting measures 5.1.
Extinguishing media 5.2. Special hazards arising from the substance or mixture 5.3. Advice for firefighters SECTION 6: Accidental release measure 6.1. Personal precautions, protective equipment and emergency procedures 6.2. Environmental precautions 6.3. Methods and material for containment and cleaning up 6.4. Reference to other sections SECTION 7: Handling and storage 7.1. Precautions for safe handling 7.2. Conditions for safe storage, including any incompatibilities 7.3. Specific end use SECTION 8: Exposure controls/personal protection 8.1. Control parameters 8.2. Exposure controls SECTION 9: Physical and chemical properties 9.1. Information on basic physical and chemical properties 9.2. Other information SECTION 10: Stability and reactivity 10.1. Reactivity 10.2. Chemical stability 10.3. Possibility of hazardous reactions 10.4. Conditions to avoid 10.5. Incompatible materials 10.6. Hazardous decomposition products SECTION 11: Toxicological information 11.1. Information on toxicological effects SECTION 12: Ecological information 12.1.
Toxicity 12.2. Persistence and degradability 12.3. Bioaccumulative potential 12.4. Mobility in soil 12.5. Results of PBT and vPvB assessment 12.6. Other adverse effects SECTION 13: Disposal considerations 13.1. Waste treatment methods SECTION 14: Transport information 14.1. UN number 14.2. UN proper shipping name 14.3. Transport hazard class 14.4. Packing group 14.5. Environmental hazards 14.6. Special precautions for user 14.7. Transport in bulk according to Annex II of MARPOL73/78 and the IBC Code SECTION 15: Regulatory information 15.1. Safety and environmental regulations/legislation specific for the substance or mixture 15.2. Chemical safety assessment SECTION 16: Other information 16.2. Date of the latest revision of the SDS In Canada, the program known as the Workplace Hazardous Materials Information System establishes the requirements for SDSs in workplaces and is administered federally by Health Canada under the Hazardous Products Act, Part II, the Controlled Products Regulations. Safety data sheets have been made an integral part of the system of Regulation No 1907/2006.
The original requirements of REACH for SDSs have been further adapted to take into account the rules for safety data sheets of the Global Harmonised System and the implementation of other elements of the GHS into EU legislation that were introduced by Regulation No 1272/2008 via an update to Annex II of REACH. The SDS must be supplied in an official language of the Member State where the substance or mixture is placed on the market, unless the Member State concerned provide otherwise; the European Chemicals Agency has published a guidance document on the compilation of safety data sheets. The German Federal Water Management Act requires that substances be evaluated for negative influence on the physical, chemical or biological characteristics of water; these are classified into numeric water hazard classes. WGK nwg: Non-water polluting substance WGK 1: Slightly water polluting substance WGK 2: Water polluting substance WGK 3: Highly water polluting substance This section contributes to a better understanding of the regulations governing SDS within the South African framework.
As regulations may change, it is the responsibility of the reader to verify the validity of the regulations mentioned in text. As globalisation increased and countries engaged in cross-border trade, the quantity of hazardous material crossing international borders a
Immediately dangerous to life or health
The term dangerous to life or health is defined by the US National Institute for Occupational Safety and Health as exposure to airborne contaminants, "likely to cause death or immediate or delayed permanent adverse health effects or prevent escape from such an environment." Examples include smoke or other poisonous gases at sufficiently high concentrations. It is calculated using the LD50 or LC50; the Occupational Safety and Health Administration regulation defines the term as "an atmosphere that poses an immediate threat to life, would cause irreversible adverse health effects, or would impair an individual's ability to escape from a dangerous atmosphere."IDLH values are used to guide the selection of breathing apparatus that are made available to workers or firefighters in specific situations. The NIOSH definition does not include oxygen deficiency although atmosphere-supplying breathing apparatus is required. Examples unventilated, confined spaces; the OSHA definition is arguably broad enough to include oxygen-deficient circumstances in the absence of "airborne contaminants", as well as many other chemical, thermal, or pneumatic hazards to life or health.
It uses the broader term "impair", rather than "prevent", with respect to the ability to escape. For example, blinding but non-toxic smoke could be considered IDLH under the OSHA definition if it would impair the ability to escape a "dangerous" but not life-threatening atmosphere; the OSHA definition is part of a legal standard, the minimum legal requirement. Users or employers are encouraged to apply proper judgment to avoid taking unnecessary risks if the only immediate hazard is "reversible", such as temporary pain, nausea, or non-toxic contamination. If the concentration of harmful substances is IDLH, the worker must use the most reliable respirators; such respirators should not use cartridges or canister with the sorbent, as their lifetime is too poorly predicted. In addition, the respirator must maintain positive pressure under the mask during inspiration, as this will prevent the leakage of unfiltered air through the gaps. Textbook NIOSH recommended for use in IDLH conditions only pressure-demand self-contained breathing apparatus with a full facepiece, or pressure-demand supplied-air respirator equipped with a full facepiece in combination with an auxiliary pressure-demand self-contained breathing apparatus.
The following examples are listed in reference to IDLH values. Legend: Ca NIOSH considers this substance to be a potential occupational carcinogen. Revised values may follow in parentheses. N. D. Not determined; that is, the level is unknown, not non-existent. 10%LEL The IDLM value has been set at 10% of the lower explosive limit although other irreversible health effects or impairment of escape due to toxicology exist only at higher levels. NIOSH air filtration rating NIOSH IDLH site 1910.134 Respiratory protection definitions