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.
Arsenic is a chemical element with symbol As and atomic number 33. Arsenic occurs in many minerals in combination with sulfur and metals, but as a pure elemental crystal. Arsenic is a metalloid, it has various allotropes, but only the gray form, which has a metallic appearance, is important to industry. The primary use of arsenic is in alloys of lead. Arsenic is a common n-type dopant in semiconductor electronic devices, the optoelectronic compound gallium arsenide is the second most used semiconductor after doped silicon. Arsenic and its compounds the trioxide, are used in the production of pesticides, treated wood products and insecticides; these applications are declining due to the toxicity of its compounds. A few species of bacteria are able to use arsenic compounds as respiratory metabolites. Trace quantities of arsenic are an essential dietary element in rats, goats and other species. A role in human metabolism is not known. However, arsenic poisoning occurs in multicellular life. Arsenic contamination of groundwater is a problem.
The United States' Environmental Protection Agency states that all forms of arsenic are a serious risk to human health. The United States' Agency for Toxic Substances and Disease Registry ranked arsenic as number 1 in its 2001 Priority List of Hazardous Substances at Superfund sites. Arsenic is classified as a Group-A carcinogen; the three most common arsenic allotropes are gray and black arsenic, with gray being the most common. Gray arsenic adopts a double-layered structure consisting of many interlocked, six-membered rings; because of weak bonding between the layers, gray arsenic is brittle and has a low Mohs hardness of 3.5. Nearest and next-nearest neighbors form a distorted octahedral complex, with the three atoms in the same double-layer being closer than the three atoms in the next; this close packing leads to a high density of 5.73 g/cm3. Gray arsenic becomes a semiconductor with a bandgap of 1.2 -- 1.4 eV if amorphized. Gray arsenic is the most stable form. Yellow arsenic is soft and waxy, somewhat similar to tetraphosphorus.
Both have four atoms arranged in a tetrahedral structure in which each atom is bound to each of the other three atoms by a single bond. This unstable allotrope, being molecular, is the most volatile, least dense, most toxic. Solid yellow arsenic is produced by rapid cooling of arsenic vapor, As4, it is transformed into gray arsenic by light. The yellow form has a density of 1.97 g/cm3. Black arsenic is similar in structure to black phosphorus. Black arsenic can be formed by cooling vapor at around 100–220 °C, it is brittle. It is a poor electrical conductor. Arsenic occurs in nature as a monoisotopic element, composed of 75As; as of 2003, at least 33 radioisotopes have been synthesized, ranging in atomic mass from 60 to 92. The most stable of these is 73As with a half-life of 80.30 days. All other isotopes have half-lives of under one day, with the exception of 71As, 72As, 74As, 76As, 77As. Isotopes that are lighter than the stable 75As tend to decay by β+ decay, those that are heavier tend to decay by β− decay, with some exceptions.
At least 10 nuclear isomers have been described, ranging in atomic mass from 66 to 84. The most stable of arsenic's isomers is 68mAs with a half-life of 111 seconds. Arsenic has a similar electronegativity and ionization energies to its lighter congener phosphorus and as such forms covalent molecules with most of the nonmetals. Though stable in dry air, arsenic forms a golden-bronze tarnish upon exposure to humidity which becomes a black surface layer; when heated in air, arsenic oxidizes to arsenic trioxide. This odor can be detected on striking arsenide minerals such as arsenopyrite with a hammer, it burns in oxygen to form arsenic trioxide and arsenic pentoxide, which have the same structure as the more well-known phosphorus compounds, in fluorine to give arsenic pentafluoride. Arsenic sublimes upon heating at atmospheric pressure, converting directly to a gaseous form without an intervening liquid state at 887 K; the triple point is 3.63 MPa and 1,090 K. Arsenic makes arsenic acid with concentrated nitric acid, arsenous acid with dilute nitric acid, arsenic trioxide with concentrated sulfuric acid.
Arsenic reacts with metals to form arsenides, though these are not ionic compounds containing the As3− ion as the formation of such an anion would be endothermic and the group 1 arsenides have properties of intermetallic compounds. Like germanium and bromine, which like arsenic succeed the 3d transition series, arsenic is much less stable in the group oxidation state of +5 than its vertical neighbors phosphorus and antimony, hence arsenic pentoxide and arsenic acid are potent oxidizers. Compounds of arsenic resemble in some respects those of phosphorus which occupies the same group of the periodic table; the most common oxidation states for arsenic are: −3 in the arsenides, which are alloy-like intermetallic compounds, +3 in the arsenites, +5 in the arsenates and most organoarsenic compounds. Arsenic bonds to itself as seen in the square As3−4 ions in the mineral skutterudite. In the +3 oxidation state, arsenic is pyramidal owing to the i
Cadet's fuming liquid
Cadet's fuming liquid was a red-brown oily liquid prepared in 1760 by the French chemist Louis Claude Cadet de Gassicourt by the reaction of potassium acetate with arsenic trioxide. It consisted of dicacodyl and cacodyl oxide; the reaction for forming the oxide was something like: 4 KCH3COO + As2O3 → 2O + 2 K2CO3 + 2 CO2These were the first organometallic substances prepared, so Cadet can be regarded as the father of organometallic chemistry. The liquid develops white fumes when exposed to air, resulting in a pale flame producing carbon dioxide and arsenic trioxide, it has a nauseating disagreeable, garlic-like odor. Around 1840, Robert Bunsen did much work on characterizing the compounds in the liquid and derivatives of them; this was important in the development of chemistry
A chemical compound is a chemical substance composed of many identical molecules composed of atoms from more than one element held together by chemical bonds. A chemical element bonded to an identical chemical element is not a chemical compound since only one element, not two different elements, is involved. There are four types of compounds, depending on how the constituent atoms are held together: molecules held together by covalent bonds ionic compounds held together by ionic bonds intermetallic compounds held together by metallic bonds certain complexes held together by coordinate covalent bonds. A chemical formula is a way of expressing information about the proportions of atoms that constitute a particular chemical compound, using the standard abbreviations for the chemical elements, subscripts to indicate the number of atoms involved. For example, water is composed of two hydrogen atoms bonded to one oxygen atom: the chemical formula is H2O. Many chemical compounds have a unique numerical identifier assigned by the Chemical Abstracts Service: its CAS number.
A compound can be converted to a different chemical composition by interaction with a second chemical compound via a chemical reaction. In this process, bonds between atoms are broken in both of the interacting compounds, bonds are reformed so that new associations are made between atoms. Any substance consisting of two or more different types of atoms in a fixed stoichiometric proportion can be termed a chemical compound, it follows from their being composed of fixed proportions of two or more types of atoms that chemical compounds can be converted, via chemical reaction, into compounds or substances each having fewer atoms. The ratio of each element in the compound is expressed in a ratio in its chemical formula. A chemical formula is a way of expressing information about the proportions of atoms that constitute a particular chemical compound, using the standard abbreviations for the chemical elements, subscripts to indicate the number of atoms involved. For example, water is composed of two hydrogen atoms bonded to one oxygen atom: the chemical formula is H2O.
In the case of non-stoichiometric compounds, the proportions may be reproducible with regard to their preparation, give fixed proportions of their component elements, but proportions that are not integral. Chemical compounds have a unique and defined chemical structure held together in a defined spatial arrangement by chemical bonds. Chemical compounds can be molecular compounds held together by covalent bonds, salts held together by ionic bonds, intermetallic compounds held together by metallic bonds, or the subset of chemical complexes that are held together by coordinate covalent bonds. Pure chemical elements are not considered chemical compounds, failing the two or more atom requirement, though they consist of molecules composed of multiple atoms. Many chemical compounds have a unique numerical identifier assigned by the Chemical Abstracts Service: its CAS number. There is varying and sometimes inconsistent nomenclature differentiating substances, which include non-stoichiometric examples, from chemical compounds, which require the fixed ratios.
Many solid chemical substances—for example many silicate minerals—are chemical substances, but do not have simple formulae reflecting chemically bonding of elements to one another in fixed ratios. It may be argued that they are related to, rather than being chemical compounds, insofar as the variability in their compositions is due to either the presence of foreign elements trapped within the crystal structure of an otherwise known true chemical compound, or due to perturbations in structure relative to the known compound that arise because of an excess of deficit of the constituent elements at places in its structure. Other compounds regarded as chemically identical may have varying amounts of heavy or light isotopes of the constituent elements, which changes the ratio of elements by mass slightly. Compounds are held together through a variety of different types of bonding and forces; the differences in the types of bonds in compounds differ based on the types of elements present in the compound.
London dispersion forces are the weakest force of all intermolecular forces. They are temporary attractive forces that form when the electrons in two adjacent atoms are positioned so that they create a temporary dipole. Additionally, London dispersion forces are responsible for condensing non polar substances to liquids, to further freeze to a solid state dependent on how low the temperature of the environment is. A covalent bond known as a molecular bond, involves the sharing of electrons between two atoms; this type of bond occurs between elements that fall close to each other on the periodic table of elements, yet it is observed between some metals and nonmetals. This is due to the mechanism of this type of bond. Elements that fall close to each other on the periodic table tend to have similar electronegativities, which means they have a similar affinity for electrons. Since neither element has a stronger affinity to donate or gain electrons, it causes the elements to share electrons so both elements have a more stable octet.
Ionic bonding occurs when valence electrons are transferred between elements. Opposite to covalent bonding, this chemical bond creates two oppositely charged ions; the metals in ionic bonding
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
Organometallic chemistry is the study of organometallic compounds, chemical compounds containing at least one chemical bond between a carbon atom of an organic molecule and a metal, including alkaline, alkaline earth, transition metals, sometimes broadened to include metalloids like boron and tin, as well. Aside from bonds to organyl fragments or molecules, bonds to'inorganic' carbon, like carbon monoxide, cyanide, or carbide, are considered to be organometallic as well; some related compounds such as transition metal hydrides and metal phosphine complexes are included in discussions of organometallic compounds, though speaking, they are not organometallic. The related but distinct term "metalorganic compound" refers to metal-containing compounds lacking direct metal-carbon bonds but which contain organic ligands. Metal β-diketonates, alkoxides and metal phosphine complexes are representative members of this class; the field of organometallic chemistry combines aspects of traditional inorganic and organic chemistry.
Organometallic compounds are used both stoichiometrically in research and industrial chemical reactions, as well as in the role of catalysts to increase the rates of such reactions, where target molecules include polymers and many other types of practical products. Organometallic compounds are distinguished by the prefix "organo-" e.g. organopalladium compounds. Examples of such organometallic compounds include all Gilman reagents, which contain lithium and copper. Tetracarbonyl nickel, ferrocene are examples of organometallic compounds containing transition metals. Other examples include organomagnesium compounds like iodomagnesium MeMgI, dimethylmagnesium, all Grignard reagents. In addition to the traditional metals, lanthanides and semimetals, elements such as boron, silicon and selenium are considered to form organometallic compounds, e.g. organoborane compounds such as triethylborane. Representative Organometallic Compounds Many complexes feature coordination bonds between a metal and organic ligands.
The organic ligands bind the metal through a heteroatom such as oxygen or nitrogen, in which case such compounds are considered coordination compounds. However, if any of the ligands form a direct M-C bond complex is considered to be organometallic, e.g. 2+. Furthermore, many lipophilic compounds such as metal acetylacetonates and metal alkoxides are called "metalorganics." A occurring transition metal alkyl complex is methylcobalamin, with a cobalt-methyl bond. This subset of complexes is discussed within the subfield of bioorganometallic chemistry. Illustrative of the many functions of the B12-dependent enzymes, the MTR enzyme catalyzes the transfer of a methyl group from a nitrogen on N5-methyl-tetrahydrofolate to the sulfur of homocysteine to produce methionine; the status of compounds in which the canonical anion has a delocalized structure in which the negative charge is shared with an atom more electronegative than carbon, as in enolates, may vary with the nature of the anionic moiety, the metal ion, the medium.
For instance, lithium enolates contain only Li-O bonds and are not organometallic, while zinc enolates contain both Zn-O and Zn-C bonds, are organometallic in nature. The metal-carbon bond in organometallic compounds is highly covalent. For electropositive elements, such as lithium and sodium, the carbon ligand exhibits carbanionic character, but free carbon-based anions are rare, an example being cyanide; as in other areas of chemistry, electron counting is useful for organizing organometallic chemistry. The 18-electron rule is helpful in predicting the stabilities of metal carbonyls and related compounds. Most organometallic compounds do not however follow the 18e rule. Chemical bonding and reactivity in organometallic compounds is discussed from the perspective of the isolobal principle; as well as X-ray diffraction, NMR and infrared spectroscopy are common techniques used to determine structure. The dynamic properties of organometallic compounds is probed with variable-temperature NMR and chemical kinetics.
Organometallic compounds undergo several important reactions: oxidative addition and reductive elimination transmetalation carbometalation hydrometalation electron transfer β-hydride elimination organometallic substitution reaction carbon-hydrogen bond activation cyclometalation migratory insertion nucleophilic abstraction Early developments in organometallic chemistry include Louis Claude Cadet's synthesis of methyl arsenic compounds related to cacodyl, William Christopher Zeise's platinum-ethylene complex, Edward Frankland's discovery of diethyl- and dimethylzinc, Ludwig Mond's discovery of Ni4, Victor Grignard's organomagnesium compounds. The abundant and diverse products from coal and petroleum led to Ziegler–Natta, Fischer–Tropsch, hydroformylation catalysis which employ CO, H2, alkenes as feedstocks and ligands. Recognition of organometalli