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Cubane-type Cluster
A cubane-type cluster is an arrangement of atoms in a molecular structure that forms a cube. In the idealized case, the eight vertices are symmetry equivalent and the species has Oh symmetry. Such a structure is illustrated by the hydrocarbon cubane. With chemical formula , cubane has carbon atoms at the corners of a cube and covalent bonds forming the edges. Most cubanes have more complicated structures, usually with nonequivalent vertices. They may be simple covalent compounds or macromolecular or supramolecular cluster compounds. Examples Other compounds having different elements in the corners, various atoms or groups bonded to the corners are all part of this class of structures. Inorganic cubane-type clusters include selenium tetrachloride, tellurium tetrachloride, and sodium silox. Cubane clusters are common throughout bioinorganic chemistry. Ferredoxins containing e4S4iron–sulfur clusters are pervasive in nature. The four iron atoms and four sulfur atoms form an alter ...
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Tetrahedral Coordination Geometry
In a tetrahedral molecular geometry, a central atom is located at the center with four substituents that are located at the corners of a tetrahedron. The bond angles are cos−1(−) = 109.4712206...° ≈ 109.5° when all four substituents are the same, as in methane () as well as its heavier analogues. Methane and other perfectly symmetrical tetrahedral molecules belong to point group Td, but most tetrahedral molecules have lower symmetry. Tetrahedral molecules can be chiral. Tetrahedral bond angle The bond angle for a symmetric tetrahedral molecule such as CH4 may be calculated using the dot product of two vectors. As shown in the diagram, the molecule can be inscribed in a cube with the tetravalent atom (e.g. carbon) at the cube centre which is the origin of coordinates, O. The four monovalent atoms (e.g. hydrogens) are at four corners of the cube (A, B, C, D) chosen so that no two atoms are at adjacent corners linked by only one cube edge. If the edge length of the cube ...
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Angle Strain
In organic chemistry, ring strain is a type of instability that exists when bonds in a molecule form angles that are abnormal. Strain is most commonly discussed for small rings such as cyclopropanes and cyclobutanes, whose internal angles are substantially smaller than the idealized value of approximately 109°. Because of their high strain, the heat of combustion for these small rings is elevated. Ring strain results from a combination of angle strain, conformational strain or Pitzer strain (torsional eclipsing interactions), and transannular strain, also known as van der Waals strain or Prelog strain. The simplest examples of angle strain are small cycloalkanes such as cyclopropane and cyclobutane. Ring strain energy can be attributed to the energy required for the distortion of bond and bond angles in order to close a ring. Ring strain energy is believed to be the cause of accelerated rates in altering ring reactions. Its interactions with traditional bond energies chan ...
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Nitrogen
Nitrogen is the chemical element with the symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at seventh in total abundance in the Milky Way and the Solar System. At standard temperature and pressure, two atoms of the element bond to form N2, a colorless and odorless diatomic gas. N2 forms about 78% of Earth's atmosphere, making it the most abundant uncombined element. Nitrogen occurs in all organisms, primarily in amino acids (and thus proteins), in the nucleic acids ( DNA and RNA) and in the energy transfer molecule adenosine triphosphate. The human body contains about 3% nitrogen by mass, the fourth most abundant element in the body after oxygen, carbon, and hydrogen. The nitrogen cycle describes the movement of the element from the air, into the biosphere and organic compounds, then back into the atmosphere. Many indus ...
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Allotrope
Allotropy or allotropism () is the property of some chemical elements to exist in two or more different forms, in the same physical state, known as allotropes of the elements. Allotropes are different structural modifications of an element: the atoms of the element are bonded together in a different manner. For example, the allotropes of carbon include diamond (the carbon atoms are bonded together to form a cubic lattice of tetrahedra), graphite (the carbon atoms are bonded together in sheets of a hexagonal lattice), graphene (single sheets of graphite), and fullerenes (the carbon atoms are bonded together in spherical, tubular, or ellipsoidal formations). The term ''allotropy'' is used for elements only, not for compounds. The more general term, used for any compound, is polymorphism, although its use is usually restricted to solid materials such as crystals. Allotropy refers only to different forms of an element within the same physical phase (the state of matter, such as ...
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Octaazacubane
Octaazacubane is a hypothetical explosive allotrope of nitrogen with formula N8, whose molecules have eight atoms arranged into a cube. (By comparison, nitrogen usually occurs as the diatomic molecule N2.) It can be regarded as a cubane-type cluster, where all eight corners are nitrogen atoms bonded along the edges. It is predicted to be a metastable molecule, in which despite the thermodynamic instability caused by bond strain, and the high energy of the N–N single bonds, the molecule remains kinetically stable for reasons of orbital symmetry. Explosive and fuel Octaazacubane is predicted to have an energy density (assuming decomposition into N2) of 22.9  MJ/ kg, which is over 5 times the standard value of TNT. It has therefore been proposed (along with other exotic nitrogen allotropes) as an explosive, and as a component of high performance rocket fuel. Its velocity of detonation is predicted to be 15,000 m/s, much (48.5%) more than octanitrocubane, the faste ...
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Tert-Butyllithium
''tert''-Butyllithium is a chemical compound with the formula (CH3)3CLi. As an organolithium compound, it has applications in organic synthesis since it is a strong base, capable of deprotonating many carbon molecules, including benzene. ''tert''-Butyllithium is available commercially as hydrocarbon solutions; it is not usually prepared in the laboratory. Preparation ''tert''-Butyllithium is produced commercially by treating ''tert''-butyl chloride with lithium metal. Its synthesis was first reported by R. B. Woodward in 1941. Structure and bonding : Like other organolithium compounds, ''tert''-butyllithium is a cluster compound. Whereas ''n''-butyllithium exists both as a hexamer and a tetramer, ''tert''-butyllithium exists exclusively as a tetramer with a cubane structure. Bonding in organolithium clusters involves sigma delocalization and significant Li−Li bonding. Despite its complicated structure, ''tert''-butyllithium is usually depicted in equations as a mono ...
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Methyllithium
Methyllithium is the simplest organolithium reagent with the empirical formula CH3Li. This s-block organometallic compound adopts an oligomeric structure both in solution and in the solid state. This highly reactive compound, invariably used in solution with an ether as the solvent, is a reagent in organic synthesis as well as organometallic chemistry. Operations involving methyllithium require anhydrous conditions, because the compound is highly reactive toward water. Oxygen and carbon dioxide are also incompatible with MeLi. Methyllithium is usually not prepared, but purchased as a solution in various ethers. Synthesis In the direct synthesis, methyl bromide is treated with a suspension of lithium in diethyl ether. :2 Li + MeBr → LiMe + LiBr The lithium bromide forms a complex with the methyllithium. Most commercially available methyllithium consists of this complex. "Halide-free" methyllithium is prepared from methyl chloride. Lithium chloride precipitates from the diethyl ...
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Tetramer
A tetramer () (''tetra-'', "four" + '' -mer'', "parts") is an oligomer formed from four monomers or subunits. The associated property is called ''tetramery''. An example from inorganic chemistry is titanium methoxide with the empirical formula Ti(OCH3)4, which is tetrameric in solid state and has the molecular formula Ti4(OCH3)16. An example from organic chemistry is kobophenol A, a substance that is formed by combining four molecules of resveratrol. In biochemistry, it similarly refers to a biomolecule formed of four units, that are the same (homotetramer), i.e. as in Concanavalin A or different (heterotetramer), i.e. as in hemoglobin. Hemoglobin has 4 similar sub-units while immunoglobulins have 2 very different sub-units. The different sub-units may have each their own activity, such as binding biotin in avidin tetramers, or have a common biological property, such as the allosteric binding of oxygen in hemoglobin. See also * Cluster chemistry; atomic and molecular clusters ...
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Alkyllithium
In organometallic chemistry, organolithium reagents are chemical compounds that contain carbon–lithium (C–Li) bonds. These reagents are important in organic synthesis, and are frequently used to transfer the organic group or the lithium atom to the substrates in synthetic steps, through nucleophilic addition or simple deprotonation. Organolithium reagents are used in industry as an initiator for anionic polymerization, which leads to the production of various elastomers. They have also been applied in asymmetric synthesis in the pharmaceutical industry. Due to the large difference in electronegativity between the carbon atom and the lithium atom, the C−Li bond is highly ionic. Owing to the polar nature of the C−Li bond, organolithium reagents are good nucleophiles and strong bases. For laboratory organic synthesis, many organolithium reagents are commercially available in solution form. These reagents are highly reactive, and are sometimes pyrophoric. History and deve ...
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Cubane
Cubane () is a synthetic hydrocarbon compound that consists of eight carbon atoms arranged at the corners of a cube, with one hydrogen atom attached to each carbon atom. A solid crystalline substance, cubane is one of the Platonic hydrocarbons and a member of the prismanes. It was first synthesized in 1964 by Philip Eaton and Thomas Cole. Before this work, Eaton believed that cubane would be impossible to synthesize due to the "required 90 degree bond angles". The cubic shape requires the carbon atoms to adopt an unusually sharp 90° bonding angle, which would be highly strained as compared to the 109.45° angle of a tetrahedral carbon. Once formed, cubane is quite kinetically stable, due to a lack of readily available decomposition paths. It is the simplest hydrocarbon with octahedral symmetry. Having high potential energy but kinetic stability makes cubane and its derivative compounds useful for controlled energy storage. For example, octanitrocubane and heptanitrocubane have ...
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Photosystem II
Photosystem II (or water-plastoquinone oxidoreductase) is the first protein complex in the light-dependent reactions of oxygenic photosynthesis. It is located in the thylakoid membrane of plants, algae, and cyanobacteria. Within the photosystem, enzymes capture photons of light to energize electrons that are then transferred through a variety of coenzymes and cofactors to reduce plastoquinone to plastoquinol. The energized electrons are replaced by oxidizing water to form hydrogen ions and molecular oxygen. By replenishing lost electrons with electrons from the splitting of water, photosystem II provides the electrons for all of photosynthesis to occur. The hydrogen ions (protons) generated by the oxidation of water help to create a proton gradient that is used by ATP synthase to generate ATP. The energized electrons transferred to plastoquinone are ultimately used to reduce to NADPH or are used in non-cyclic electron flow. DCMU is a chemical often used in laboratory sett ...
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