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
An odor, or odour, is caused by one or more volatilized chemical compounds that are found in low concentrations that humans and animals can perceive by their sense of smell. An odor is called a "smell" or a "scent", which can refer to either a pleasant or an unpleasant odor. While "scent" can refer to pleasant and unpleasant odors, the terms "scent", "aroma", "fragrance" are reserved for pleasant-smelling odors and are used in the food and cosmetic industry to describe floral scents or to refer to perfumes. In the United Kingdom, "odour" refers to scents in general. An unpleasant odor can be described as "reeking" or called a "malodor", "stench", "pong", or "stink"; the perception of odors, or sense of smell, is mediated by the olfactory nerve. The olfactory receptor cells are neurons present in the olfactory epithelium, a small patch of tissue at the back of the nasal cavity. There are millions of olfactory receptor neurons; each neuron has cilia in direct contact with the air. Odorous molecules bind to receptor proteins extending from cilia and act as a chemical stimulus, initiating electric signals that travel along the olfactory nerve's axons to the brain.
When an electrical signal reaches a threshold, the neuron fires, which sends a signal traveling along the axon to the olfactory bulb, a part of the limbic system of the brain. Interpretation of the smell begins there, relating the smell to past experiences and in relation to the substance inhaled; the olfactory bulb acts as a relay station connecting the nose to the olfactory cortex in the brain. Olfactory information is further processed and forwarded to the central nervous system, which controls emotions and behavior as well as basic thought processes. Odor sensation depends on the concentration available to the olfactory receptors. A single odorant is recognized by many receptors. Different odorants are recognized by combinations of receptors; the patterns of neuron signals help to identify the smell. The olfactory system does not interpret a single compound, but instead the whole odorous mix; this does not correspond to the intensity of any single constituent. Most odors consists of organic compounds, although some simple compounds not containing carbon, such as hydrogen sulfide and ammonia, are odorants.
The perception of an odor effect is a two-step process. First, there is the physiological part; this is the detection of stimuli by receptors in the nose. The stimuli are recognized by the region of the human brain; because of this, an objective and analytical measure of odor is impossible. While odor feelings are personal perceptions, individual reactions are related, they relate to things such as gender, state of health, personal history. The ability to identify odor varies among decreases with age. Studies show there are sex differences in odor discrimination, women outperform men. Pregnant women have increased smell sensitivity, sometimes resulting in abnormal taste and smell perceptions, leading to food cravings or aversions; the ability to taste decreases with age as the sense of smell tends to dominate the sense of taste. Chronic smell problems are reported in small numbers for those in their mid-twenties, with numbers increasing with overall sensitivity beginning to decline in the second decade of life, deteriorating appreciably as age increases once over 70 years of age.
For most untrained people, the process of smelling gives little information concerning the specific ingredients of an odor. Their smell perception offers information related to the emotional impact. Experienced people, such as flavorists and perfumers, can pick out individual chemicals in complex mixtures through smell alone. Odor perception is a primal sense; the sense of smell enables pleasure, can subconsciously warn of danger, help locate mates, find food, or detect predators. Humans have a good sense of smell, correlated to an evolutionary decline in sense of smell. A human's sense of smell is just as good as many animals and can distinguish a diversity of odors—approximately 10,000 scents. Studies reported. Odors that a person is used to, such as their own body odor, are less noticeable than uncommon odors; this is due to habituation. After continuous odor exposure, the sense of smell is fatigued, but recovers if the stimulus is removed for a time. Odors can change due to environmental conditions: for example, odors tend to be more distinguishable in cool dry air.
Habituation affects the ability to distinguish odors after continuous exposure. The sensitivity and ability to discriminate odors diminishes with exposure, the brain tends to ignore continuous stimulus and focus on differences and changes in a particular sensation; when odorants are mixed, a habitual odorant is blocked. This depends on the strength of the odorants in the mixture, which can change the perception and processing of an odor; this process helps classify similar odors as well as adjust sensitivity to differences in complex stimuli. The primary gene sequences for thousands of olfactory receptors are known for the genomes of more than a dozen organisms, they are seven-helix-turn transmembrane proteins. But there are no known structures for any olfactory receptor. There is a conserved sequence in three quarters of all ORs; this is a tripodal metal-ion binding site, and
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.
The boiling point of a substance is the temperature at which the vapor pressure of a liquid equals the pressure surrounding the liquid and the liquid changes into a vapor. The boiling point of a liquid varies depending upon the surrounding environmental pressure. A liquid in a partial vacuum has a lower boiling point than when that liquid is at atmospheric pressure. A liquid at high pressure has a higher boiling point than when that liquid is at atmospheric pressure. For example, water at 93.4 °C at 1,905 metres altitude. For a given pressure, different liquids will boil at different temperatures; the normal boiling point of a liquid is the special case in which the vapor pressure of the liquid equals the defined atmospheric pressure at sea level, 1 atmosphere. At that temperature, the vapor pressure of the liquid becomes sufficient to overcome atmospheric pressure and allow bubbles of vapor to form inside the bulk of the liquid; 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 liquid's 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, resulting in the formation of vapor bubbles within the liquid. A saturated liquid contains as much thermal energy. Saturation temperature means boiling point; 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 thermal 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.
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 vapor pressure of the liquid equals the surrounding environmental pressure. Thus, the boiling point is dependent on the pressure. Boiling points may be published with respect to the NIST, USA standard pressure of 101.325 kPa, or the IUPAC standard pressure of 100.000 kPa. At higher elevations, where the atmospheric pressure is much lower, the boiling point is lower; the boiling point increases with increased pressure up to the critical point, where the gas and liquid properties become identical. The boiling point cannot be increased beyond the critical point; the boiling point decreases with decreasing pressure until the triple point is reached. The boiling point cannot be reduced below the triple point. If the heat of vaporization and the vapor pressure of a liquid at a certain temperature are known, the boiling point can be calculated by using the Clausius–Clapeyron equation, thus: T B = − 1, where: T B is the boiling point at the pressure of interest, R is the ideal gas constant, P is the vapour pressure of the liquid at the pressure of interest, P 0 is some pressure where the corresponding T 0 is known, Δ H vap is the heat of vaporization of the liquid, T 0 is the boiling temperature, ln is the natural logarithm.
Saturation pressure is the pressure for a corresponding saturation temperature at which a liquid boils into its vapor phase. Saturation pressure and saturation temperature have a direct relationship: as saturation pressure is increased, so is saturation temperature. If the temperature in a system remains constant, vapor at saturation pressure and temperature will begin to condense into its liquid phase as the system pressure is increased. A liquid at saturation pressure and temperature will tend to flash into its vapor phase as system pressure is decreased. There are two conventions regarding the standard boiling point of water: The normal boiling point is 99.97 °C at a pressure of 1 atm. The IUPAC recommended standard boiling point of water at a standard pressure of 100 kPa is 99.61 °C. For comparison, on top of Mount Everest, at 8,848 m elevation, the pressure is about 34 kPa and the boiling point of water is 71 °C; the Celsius temperature scale was defined until 1954 by two points: 0 °C being defined by the wate
Chloroform, or trichloromethane, is an organic compound with formula CHCl3. It is a colorless, sweet-smelling, dense liquid, produced on a large scale as a precursor to PTFE, it is a precursor to various refrigerants. It is one of a trihalomethane, it is a powerful anesthetic, euphoriant and sedative when inhaled or ingested. The molecule adopts a tetrahedral molecular geometry with C3v symmetry; the total global flux of chloroform through the environment is 660000 tonnes per year, about 90% of emissions are natural in origin. Many kinds of seaweed produce chloroform, fungi are believed to produce chloroform in soil. Abiotic process is believed to contribute to natural chloroform productions in soils although the mechanism is still unclear. Chloroform volatilizes from soil and surface water and undergoes degradation in air to produce phosgene, formyl chloride, carbon monoxide, carbon dioxide, hydrogen chloride, its half-life in air ranges from 55 to 620 days. Biodegradation in water and soil is slow.
Chloroform does not bioaccumulate in aquatic organisms. Chloroform was synthesized independently by several investigators circa 1831: Moldenhawer, a German pharmacist from Frankfurt an der Oder, appears to have produced chloroform in 1830 by mixing chlorinated lime with ethanol. Samuel Guthrie, an American physician from Sackets Harbor, New York appears to have produced chloroform in 1831 by reacting chlorinated lime with ethanol, as well as noting its anaesthetic properties. Justus von Liebig carried out the alkaline cleavage of chloral. Eugène Soubeiran obtained the compound by the action of chlorine bleach on both acetone. In 1834, French chemist Jean-Baptiste Dumas named it. In 1835, Dumas prepared the substance by the alkaline cleavage of trichloroacetic acid. Regnault prepared chloroform by chlorination of chloromethane. In 1842, Robert Mortimer Glover in London discovered the anaesthetic qualities of chloroform on laboratory animals. In 1847, Scottish obstetrician James Y. Simpson was the first to demonstrate the anaesthetic properties of chloroform on humans and helped to popularise the drug for use in medicine.
By the 1850s, chloroform was being produced on a commercial basis by using the Liebig procedure, which retained its importance until the 1960s. Today, chloroform — along with dichloromethane — is prepared and on a massive scale by the chlorination of methane and chloromethane. In industry, chloroform is produced by heating a mixture of chlorine and either chloromethane or methane. At 400–500 °C, a free radical halogenation occurs, converting these precursors to progressively more chlorinated compounds: CH4 + Cl2 → CH3Cl + HCl CH3Cl + Cl2 → CH2Cl2 + HCl CH2Cl2 + Cl2 → CHCl3 + HClChloroform undergoes further chlorination to yield carbon tetrachloride: CHCl3 + Cl2 → CCl4 + HClThe output of this process is a mixture of the four chloromethanes, which can be separated by distillation. Chloroform may be produced on a small scale via the haloform reaction between acetone and sodium hypochlorite: 3 NaClO + 2CO → CHCl3 + 2 NaOH + NaOCOCH3 Deuterated chloroform is an isotopologue of chloroform with a single deuterium atom.
CDCl3 is a common solvent used in NMR spectroscopy. Deuterochloroform is produced by the haloform reaction, the reaction of acetone with sodium hypochlorite or calcium hypochlorite; the haloform process is now obsolete for the production of ordinary chloroform. Deuterochloroform can be prepared by the reaction of sodium deuteroxide with chloral hydrate; the haloform reaction can occur inadvertently in domestic settings. Bleaching with hypochlorite generates halogenated compounds in side reactions. Sodium hypochlorite solution mixed with common household liquids such as acetone, methyl ethyl ketone, ethanol, or isopropyl alcohol can produce some chloroform, in addition to other compounds such as chloroacetone or dichloroacetone. In terms of scale, the most important reaction of chloroform is with hydrogen fluoride to give monochlorodifluoromethane, a precursor in the production of polytetrafluoroethylene: CHCl3 + 2 HF → CHClF2 + 2 HClThe reaction is conducted in the presence of a catalytic amount of mixed antimony halides.
Chlorodifluoromethane is converted into tetrafluoroethylene, the main precursor to Teflon. Before the Montreal Protocol, chlorodifluoromethane was a popular refrigerant; the hydrogen attached to carbon in chloroform participates in hydrogen bonding. Worldwide, chloroform is used in pesticide formulations, as a solvent for fats, rubber, waxes, gutta-percha, resins, as a cleansing agent, grain fumigant, in fire extinguishers, in the rubber industry. CDCl3 is a common solvent used in NMR spectroscopy; as a reagent, chloroform serves as a source of the dichlorocarbene CCl2 group. It reacts with aqueous sodium hydroxide in the presence of a phase transfer catalyst to produce dichlorocarbene, CCl2; this reagent effects ortho-formylation of activated aromatic rings such as phenols, producing aryl aldehydes in a reaction known as the Reimer–Tiemann reaction. Alternatively, the carbene can be trapped by an alkene to form a cyclopropane derivative. In the Kharasch addition, chloroform forms the CHCl2 free radical in addition to alkenes.
The anaesthetic qualities of chloroform were first described in 1842 in a thesis by Robert Mortimer Glover, which won t
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
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