High-valent iron denotes compounds and intermediates in which iron is found in a formal oxidation state > 3 that show a number of bonds > 6 with a coordination number ≤ 6. The term is rather uncommon for hepta-coordinate compounds of iron, it has to be distinguished from the terms hypervalent and hypercoordinate, as high-valent iron compounds neither violate the 18-electron rule nor show coordination numbers > 6. The ferrate ion 2− was the first structure in this class synthesized; the synthetic compounds discussed below contain oxidized iron in general, as the concepts are related. Oxoferryl species are proposed as intermediates in catalytic cycles biological systems in which O2 activation is required. Diatomic oxygen has a high reduction potential, but the first step required to harness this potential is a thermodynamically unfavorable one electron reduction E0 = -0.16 V. This reduction occurs in nature by the formation of a superoxide complex in which a reduced metal is oxidized by O2; the product of this reaction is a peroxide radical, more reactive.
The abundance of these species in nature and the chemistry, available to them are the reasons why the study of these compounds is important. A applicable method for the generation of high-valent oxoferryl species is the oxidation with iodosobenzene: F e n + O I P h ⟶ F e n + 2 O + I P h symbolic oxidation of an iron compound using iodosobenzene; these compounds model biological complexes such as cytochrome P450, NO synthase, isopenicillin N synthase. Two such reported compounds are cyclam-acetate oxoiron. Thiolate-ligated oxoiron is formed by the oxidation of a precursor, 3-5 equivalents of H2O2 at -60 ˚C in methanol; the iron compound is deep blue in color and shows intense absorption features at 460 nm, 570 nm, 850 nm, 1050 nm. This species FeIV + is stable at -60 ˚C. Compound 2 was identified by Mössbauer spectroscopy, high resolution electrospray ionization mass spectrometry, X-ray absorption spectroscopy, extended X-ray absorption fine structure, ultraviolet–visible spectroscopy, Fourier-transform infrared spectroscopy, results were compared to density functional theory calculations.
Tetramethylcyclam oxoiron is formed by the reaction of FeII2, TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane. A second method for formation of cyclam oxoiron is reported as the reaction of FeII2 with 3 equivalents of H2O2 for 3 hours; this species has an absorption maximum at 820 nm. It is reported to be stable for at least 1 month at -40 ˚C, it has been characterized by Mössbauer spectroscopy, ESI-MS, EXAFS, UV-vis, Raman spectroscopy, FT-IR. High-valent iron bispidine complexes can oxidize cyclohexane to cyclohexanol and cyclohexanone in 35% yield with an alcohol to ketone ratio up to 4. FeVTAML, TAML = tetra-amido macrocyclic ligand, is formed by the reaction of with 2-5 equivalents of meta-chloroperbenzoic acid at -60 ˚C in n-butyronitrile; this deep green compound is stable at 77 K. The stabilization of Fe is attributed to the strong π–donor capacity of deprotonated amide nitrogens; the electronic structure of porphyrin oxoiron compounds has been reviewed. Nitridoiron and imidoiron compounds are related to iron-dinitrogen chemistry.
The biological significance of nitridoiron porphyrins has been reviewed. A applicable method to generate high-valent nitridoiron species is the thermal or photochemical oxidative elimination of molecular nitrogen from an azide complex. F e n N 3 ⟶ F e n + 2 N + N 2 symbolic oxidative elimination of nitrogen yields a nitridoiron complex; the first nitridoiron compound was generated and characterized in 1988/1989 by Wagner and Nakamoto using photolysis and Raman spectroscopy at low temperatures. A second FeVI species apart from 2, has been reported; this species, is formed by oxidation followed by photolysis to yield the Fe species. Characterization of the Fe complex was done by Mossbauer, EXAFS, IR, DFT calculations. Unlike the ferrate ion, compound 5 is diamagnetic. Bridged µ-nitrido di-iron phthalocyanine compounds catalyze the oxidation of methane to methanol and formic acid using hydrogen peroxide as sacrificial oxidant. Nitridoiron and nitridoiron species were first explored theoretically in 2002.
Jacobsen's catalyst Solomon et al..
Paramagnetism is a form of magnetism whereby certain materials are weakly attracted by an externally applied magnetic field, form internal, induced magnetic fields in the direction of the applied magnetic field. In contrast with this behavior, diamagnetic materials are repelled by magnetic fields and form induced magnetic fields in the direction opposite to that of the applied magnetic field. Paramagnetic materials include some compounds; the magnetic moment induced by the applied field is rather weak. It requires a sensitive analytical balance to detect the effect and modern measurements on paramagnetic materials are conducted with a SQUID magnetometer. Paramagnetism is due to the presence of unpaired electrons in the material, so all atoms with incompletely filled atomic orbitals are paramagnetic. Due to their spin, unpaired electrons have a magnetic dipole act like tiny magnets. An external magnetic field causes the electrons' spins to align parallel to the field, causing a net attraction.
Paramagnetic materials include aluminium, oxygen and iron oxide. Unlike ferromagnets, paramagnets do not retain any magnetization in the absence of an externally applied magnetic field because thermal motion randomizes the spin orientations, thus the total magnetization drops to zero. In the presence of the field there is only a small induced magnetization because only a small fraction of the spins will be oriented by the field; this fraction is proportional to the field strength and this explains the linear dependency. The attraction experienced by ferromagnetic materials is non-linear and much stronger, so that it is observed, for instance, in the attraction between a refrigerator magnet and the iron of the refrigerator itself. Constituent atoms or molecules of paramagnetic materials have permanent magnetic moments in the absence of an applied field; the permanent moment is due to the spin of unpaired electrons in atomic or molecular electron orbitals. In pure paramagnetism, the dipoles do not interact with one another and are randomly oriented in the absence of an external field due to thermal agitation, resulting in zero net magnetic moment.
When a magnetic field is applied, the dipoles will tend to align with the applied field, resulting in a net magnetic moment in the direction of the applied field. In the classical description, this alignment can be understood to occur due to a torque being provided on the magnetic moments by an applied field, which tries to align the dipoles parallel to the applied field. However, the true origins of the alignment can only be understood via the quantum-mechanical properties of spin and angular momentum. If there is sufficient energy exchange between neighbouring dipoles, they will interact, may spontaneously align or anti-align and form magnetic domains, resulting in ferromagnetism or antiferromagnetism, respectively. Paramagnetic behavior can be observed in ferromagnetic materials that are above their Curie temperature, in antiferromagnets above their Néel temperature. At these temperatures, the available thermal energy overcomes the interaction energy between the spins. In general, paramagnetic effects are quite small: the magnetic susceptibility is of the order of 10−3 to 10−5 for most paramagnets, but may be as high as 10−1 for synthetic paramagnets such as ferrofluids.
In conductive materials, the electrons are delocalized, that is, they travel through the solid more or less as free electrons. Conductivity can be understood in a band structure picture as arising from the incomplete filling of energy bands. In an ordinary nonmagnetic conductor the conduction band is identical for both spin-up and spin-down electrons; when a magnetic field is applied, the conduction band splits apart into a spin-up and a spin-down band due to the difference in magnetic potential energy for spin-up and spin-down electrons. Since the Fermi level must be identical for both bands, this means that there will be a small surplus of the type of spin in the band that moved downwards; this effect is a weak form of paramagnetism known as Pauli paramagnetism. The effect always competes with a diamagnetic response of opposite sign due to all the core electrons of the atoms. Stronger forms of magnetism require localized rather than itinerant electrons. However, in some cases a band structure can result in which there are two delocalized sub-bands with states of opposite spins that have different energies.
If one subband is preferentially filled over the other, one can have itinerant ferromagnetic order. This situation only occurs in narrow bands, which are poorly delocalized. Strong delocalization in a solid due to large overlap with neighboring wave functions means that there will be a large Fermi velocity; this is why s- and p-type metals are either Pauli-paramagnetic or as in the case of gold diamagnetic. In the latter case the diamagnetic contribution from the closed shell inner electrons wins over the weak paramagnetic term of the free electrons. Stronger magnetic effects are only observed when d or f electrons are involved; the latter are strongly localized. Moreover, the size of the magnetic
Water is a transparent, tasteless and nearly colorless chemical substance, the main constituent of Earth's streams and oceans, the fluids of most living organisms. It is vital for all known forms of life though it provides no calories or organic nutrients, its chemical formula is H2O, meaning that each of its molecules contains one oxygen and two hydrogen atoms, connected by covalent bonds. Water is the name of the liquid state of H2O at standard ambient pressure, it forms precipitation in the form of rain and aerosols in the form of fog. Clouds are formed from suspended droplets of its solid state; when finely divided, crystalline ice may precipitate in the form of snow. The gaseous state of water is water vapor. Water moves continually through the water cycle of evaporation, condensation and runoff reaching the sea. Water covers 71% of the Earth's surface in seas and oceans. Small portions of water occur as groundwater, in the glaciers and the ice caps of Antarctica and Greenland, in the air as vapor and precipitation.
Water plays an important role in the world economy. 70% of the freshwater used by humans goes to agriculture. Fishing in salt and fresh water bodies is a major source of food for many parts of the world. Much of long-distance trade of commodities and manufactured products is transported by boats through seas, rivers and canals. Large quantities of water and steam are used for cooling and heating, in industry and homes. Water is an excellent solvent for a wide variety of chemical substances. Water is central to many sports and other forms of entertainment, such as swimming, pleasure boating, boat racing, sport fishing, diving; the word water comes from Old English wæter, from Proto-Germanic *watar, from Proto-Indo-European *wod-or, suffixed form of root *wed-. Cognate, through the Indo-European root, with Greek ύδωρ, Russian вода́, Irish uisce, Albanian ujë; the identification of water as a substance Water is a polar inorganic compound, at room temperature a tasteless and odorless liquid, nearly colorless with a hint of blue.
This simplest hydrogen chalcogenide is by far the most studied chemical compound and is described as the "universal solvent" for its ability to dissolve many substances. This allows it to be the "solvent of life", it is the only common substance to exist as a solid and gas in normal terrestrial conditions. Water is a liquid at the pressures that are most adequate for life. At a standard pressure of 1 atm, water is a liquid between 0 and 100 °C. Increasing the pressure lowers the melting point, about −5 °C at 600 atm and −22 °C at 2100 atm; this effect is relevant, for example, to ice skating, to the buried lakes of Antarctica, to the movement of glaciers. Increasing the pressure has a more dramatic effect on the boiling point, about 374 °C at 220 atm; this effect is important in, among other things, deep-sea hydrothermal vents and geysers, pressure cooking, steam engine design. At the top of Mount Everest, where the atmospheric pressure is about 0.34 atm, water boils at 68 °C. At low pressures, water cannot exist in the liquid state and passes directly from solid to gas by sublimation—a phenomenon exploited in the freeze drying of food.
At high pressures, the liquid and gas states are no longer distinguishable, a state called supercritical steam. Water differs from most liquids in that it becomes less dense as it freezes; the maximum density of water in its liquid form is 1,000 kg/m3. The density of ice is 917 kg/m3. Thus, water expands 9% in volume as it freezes, which accounts for the fact that ice floats on liquid water; the details of the exact chemical nature of liquid water are not well understood. Pure water is described as tasteless and odorless, although humans have specific sensors that can feel the presence of water in their mouths, frogs are known to be able to smell it. However, water from ordinary sources has many dissolved substances, that may give it varying tastes and odors. Humans and other animals have developed senses that enable them to evaluate the potability of water by avoiding water, too salty or putrid; the apparent color of natural bodies of water is determined more by dissolved and suspended solids, or by reflection of the sky, than by water itself.
Light in the visible electromagnetic spectrum can traverse a couple meters of pure water without significant absorption, so that it looks transparent and colorless. Thus aquatic plants and other photosynthetic organisms can live in water up to hundreds of meters deep, because sunlight can reach them. Water vapour is invisible as a gas. Through a thickness of 10 meters or more, the intrinsic color of water is visibly turquoise, as its absorption spectrum has
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.
Redox is a chemical reaction in which the oxidation states of atoms are changed. Any such reaction involves both a reduction process and a complementary oxidation process, two key concepts involved with electron transfer processes. Redox reactions include all chemical reactions; the chemical species from which the electron is stripped is said to have been oxidized, while the chemical species to which the electron is added is said to have been reduced. It can be explained in simple terms: Oxidation is the loss of electrons or an increase in oxidation state by a molecule, atom, or ion. Reduction is a decrease in oxidation state by a molecule, atom, or ion; as an example, during the combustion of wood, oxygen from the air is reduced, gaining electrons from carbon, oxidized. Although oxidation reactions are associated with the formation of oxides from oxygen molecules, oxygen is not included in such reactions, as other chemical species can serve the same function; the reaction can occur slowly, as with the formation of rust, or more in the case of fire.
There are simple redox processes, such as the oxidation of carbon to yield carbon dioxide or the reduction of carbon by hydrogen to yield methane, more complex processes such as the oxidation of glucose in the human body. "Redox" is a portmanteau of the words "reduction" and "oxidation". The word oxidation implied reaction with oxygen to form an oxide, since dioxygen was the first recognized oxidizing agent; the term was expanded to encompass oxygen-like substances that accomplished parallel chemical reactions. The meaning was generalized to include all processes involving loss of electrons; the word reduction referred to the loss in weight upon heating a metallic ore such as a metal oxide to extract the metal. In other words, ore was "reduced" to metal. Antoine Lavoisier showed. Scientists realized that the metal atom gains electrons in this process; the meaning of reduction became generalized to include all processes involving a gain of electrons. Though "reduction" seems counter-intuitive when speaking of the gain of electrons, it might help to think of reduction as the loss of oxygen, its historical meaning.
Since electrons are negatively charged, it is helpful to think of this as reduction in electrical charge. The electrochemist John Bockris has used the words electronation and deelectronation to describe reduction and oxidation processes when they occur at electrodes; these words are analogous to protonation and deprotonation, but they have not been adopted by chemists worldwide. The term "hydrogenation" could be used instead of reduction, since hydrogen is the reducing agent in a large number of reactions in organic chemistry and biochemistry. But, unlike oxidation, generalized beyond its root element, hydrogenation has maintained its specific connection to reactions that add hydrogen to another substance; the word "redox" was first used in 1928. The processes of oxidation and reduction occur and cannot happen independently of one another, similar to the acid–base reaction; the oxidation alone and the reduction alone are each called a half-reaction, because two half-reactions always occur together to form a whole reaction.
When writing half-reactions, the gained or lost electrons are included explicitly in order that the half-reaction be balanced with respect to electric charge. Though sufficient for many purposes, these general descriptions are not correct. Although oxidation and reduction properly refer to a change in oxidation state — the actual transfer of electrons may never occur; the oxidation state of an atom is the fictitious charge that an atom would have if all bonds between atoms of different elements were 100% ionic. Thus, oxidation is best defined as an increase in oxidation state, reduction as a decrease in oxidation state. In practice, the transfer of electrons will always cause a change in oxidation state, but there are many reactions that are classed as "redox" though no electron transfer occurs. In redox processes, the reductant transfers electrons to the oxidant. Thus, in the reaction, the reductant or reducing agent loses electrons and is oxidized, the oxidant or oxidizing agent gains electrons and is reduced.
The pair of an oxidizing and reducing agent that are involved in a particular reaction is called a redox pair. A redox couple is a reducing species and its corresponding oxidizing form, e.g. Fe2+/Fe3+ Substances that have the ability to oxidize other substances are said to be oxidative or oxidizing and are known as oxidizing agents, oxidants, or oxidizers; that is, the oxidant removes electrons from another substance, is thus itself reduced. And, because it "accepts" electrons, the oxidizing agent is called an electron acceptor. Oxygen is the quintessential oxidizer. Oxidants are chemical substances with elements in high oxidation states, or else electronegative elements that can gain extra electrons by oxidizing another substance. Substances that have the ability to reduce other substances are said to be reductive or reducing and are known as
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
Inorganic chemistry deals with the synthesis and behavior of inorganic and organometallic compounds. This field covers all chemical compounds except the myriad organic compounds, which are the subjects of organic chemistry; the distinction between the two disciplines is far from absolute, as there is much overlap in the subdiscipline of organometallic chemistry. It has applications in every aspect of the chemical industry, including catalysis, materials science, surfactants, medications and agriculture. Many inorganic compounds are ionic compounds, consisting of cations and anions joined by ionic bonding. Examples of salts are magnesium chloride MgCl2, which consists of magnesium cations Mg2+ and chloride anions Cl−. In any salt, the proportions of the ions are such that the electric charges cancel out, so that the bulk compound is electrically neutral; the ions are described by their oxidation state and their ease of formation can be inferred from the ionization potential or from the electron affinity of the parent elements.
Important classes of inorganic compounds are the oxides, the carbonates, the sulfates, the halides. Many inorganic compounds are characterized by high melting points. Inorganic salts are poor conductors in the solid state. Other important features include their high melting ease of crystallization. Where some salts are soluble in water, others are not; the simplest inorganic reaction is double displacement when in mixing of two salts the ions are swapped without a change in oxidation state. In redox reactions one reactant, the oxidant, lowers its oxidation state and another reactant, the reductant, has its oxidation state increased; the net result is an exchange of electrons. Electron exchange can occur indirectly as well, e.g. in batteries, a key concept in electrochemistry. When one reactant contains hydrogen atoms, a reaction can take place by exchanging protons in acid-base chemistry. In a more general definition, any chemical species capable of binding to electron pairs is called a Lewis acid.
As a refinement of acid-base interactions, the HSAB theory takes into account polarizability and size of ions. Inorganic compounds are found in nature as minerals. Soil may contain iron sulfide as calcium sulfate as gypsum. Inorganic compounds are found multitasking as biomolecules: as electrolytes, in energy storage or in construction; the first important man-made inorganic compound was ammonium nitrate for soil fertilization through the Haber process. Inorganic compounds are synthesized for use as catalysts such as vanadium oxide and titanium chloride, or as reagents in organic chemistry such as lithium aluminium hydride. Subdivisions of inorganic chemistry are organometallic chemistry, cluster chemistry and bioinorganic chemistry; these fields are active areas of research in inorganic chemistry, aimed toward new catalysts and therapies. Inorganic chemistry is a practical area of science. Traditionally, the scale of a nation's economy could be evaluated by their productivity of sulfuric acid.
The top 20 inorganic chemicals manufactured in Canada, Europe, India and the US:Aluminium sulfate, Ammonium nitrate, Ammonium sulfate, Carbon black, hydrochloric acid, hydrogen peroxide, nitric acid, oxygen, phosphoric acid, sodium carbonate, sodium chlorate, sodium hydroxide, sodium silicate, sodium sulfate, sulfuric acid, titanium dioxide. The manufacturing of fertilizers is another practical application of industrial inorganic chemistry. Descriptive inorganic chemistry focuses on the classification of compounds based on their properties; the classification focuses on the position in the periodic table of the heaviest element in the compound by grouping compounds by their structural similarities. When studying inorganic compounds, one encounters parts of the different classes of inorganic chemistry. Different classifications are: Classical coordination compounds feature metals bound to "lone pairs" of electrons residing on the main group atoms of ligands such as H2O, NH3, Cl−, CN−. In modern coordination compounds all organic and inorganic compounds can be used as ligands.
The "metal" is a metal from the groups 3-13, as well as the trans-lanthanides and trans-actinides, but from a certain perspective, all chemical compounds can be described as coordination complexes. The stereochemistry of coordination complexes can be quite rich, as hinted at by Werner's separation of two enantiomers of 6+, an early demonstration that chirality is not inherent to organic compounds. A topical theme within this specialization is supramolecular coordination chemistry. Examples: −, 3+, TiCl42; these species feature elements from groups II, III, IV, V, VI, VII, 0 of the periodic table. Due to their similar reactivity, the elements in group 3 and group 12 are generally included, the lanthanides and actinides are sometimes included as well. Main group compounds have been known since the beginnings of chemistry, e.g. elemental sulfur and the distillable white phosphorus. Experiments on oxygen, O2, by Lavoisier and Priestley not only iden