Cubane-type cluster

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Tellurium tetrachloride, illustrative cubane cluster. Tellurium-tetrachloride-tetramer-from-xtal-2000-3D-balls.png
Tellurium tetrachloride, illustrative cubane 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 [Fe4S4] iron–sulfur clusters are pervasive in nature. [1] The four iron atoms and four sulfur atoms form an alternating arrangement at the corners. The whole cluster is typically anchored by coordination of the iron atoms, usually with cysteine residues. In this way, each Fe center achieves tetrahedral coordination geometry. Some [Fe4S4] clusters arise via dimerization of square-shaped [Fe2S2] precursors. Many synthetic analogues are known including heterometallic derivatives. [2]

Several alkyllithium compounds exist as clusters in solution, typically tetramers, with the formula [RLi]4. Examples include methyllithium and tert-butyllithium. The individual RLi molecules are not observed. The four lithium atoms and the carbon from each alkyl group bonded to them occupy alternating vertices of the cube, with the additional atoms of the alkyl groups projecting off their respective corners. [5]

Octaazacubane is a hypothetical allotrope of nitrogen with formula N8; the nitrogen atoms are the corners of the cube. Like the carbon-based cubane compounds, octaazacubane is predicted to be highly unstable due to angle strain at the corners, and it also does not enjoy the kinetic stability seen for its organic analogues. [6]

Related Research Articles

Carbide Inorganic compound group

In chemistry, a carbide usually describes a compound composed of carbon and a metal. In metallurgy, carbiding or carburizing is the process for producing carbide coatings on a metal piece.

Carbon compounds are defined as chemical substances containing carbon. More compounds of carbon exist than any other chemical element except for hydrogen. Organic carbon compounds are far more numerous than inorganic carbon compounds. In general bonds of carbon with other elements are covalent bonds. Carbon is tetravalent but carbon free radicals and carbenes occur as short-lived intermediates. Ions of carbon are carbocations and carbanions are also short-lived. An important carbon property is catenation as the ability to form long carbon chains and rings.

Iron–sulfur cluster

Iron–sulfur clusters are molecular ensembles of iron and sulfide. They are most often discussed in the context of the biological role for iron–sulfur proteins, which are pervasive. Many Fe–S clusters are known in the area of organometallic chemistry and as precursors to synthetic analogues of the biological clusters. It is believed that the last universal common ancestor had many iron-sulfur clusters.

Titanium tetrachloride Inorganic chemical compound

Titanium tetrachloride is the inorganic compound with the formula TiCl4. It is an important intermediate in the production of titanium metal and the pigment titanium dioxide. TiCl4 is a volatile liquid. Upon contact with humid air, it forms thick clouds of titanium dioxide (TiO2) and hydrochloric acid, a reaction formerly exploited to produce fake smoke on film sets. It is sometimes referred to as "tickle" or "tickle 4" due to the phonetic resemblance of its molecular formula (TiCl4) to the word.

Ferredoxins are iron–sulfur proteins that mediate electron transfer in a range of metabolic reactions. The term "ferredoxin" was coined by D.C. Wharton of the DuPont Co. and applied to the "iron protein" first purified in 1962 by Mortenson, Valentine, and Carnahan from the anaerobic bacterium Clostridium pasteurianum.

Atom cluster

In chemistry, an atom cluster is an ensemble of bound atoms or molecules that is intermediate in size between a simple molecule and a nanoparticle; that is, up to a few nanometers (nm) in diameter. The term microcluster may be used for ensembles with up to couple dozen atoms.

Iron–sulfur proteins are proteins characterized by the presence of iron–sulfur clusters containing sulfide-linked di-, tri-, and tetrairon centers in variable oxidation states. Iron–sulfur clusters are found in a variety of metalloproteins, such as the ferredoxins, as well as NADH dehydrogenase, hydrogenases, coenzyme Q – cytochrome c reductase, succinate – coenzyme Q reductase and nitrogenase. Iron–sulfur clusters are best known for their role in the oxidation-reduction reactions of electron transport in mitochondria and chloroplasts. Both Complex I and Complex II of oxidative phosphorylation have multiple Fe–S clusters. They have many other functions including catalysis as illustrated by aconitase, generation of radicals as illustrated by SAM-dependent enzymes, and as sulfur donors in the biosynthesis of lipoic acid and biotin. Additionally, some Fe–S proteins regulate gene expression. Fe–S proteins are vulnerable to attack by biogenic nitric oxide, forming dinitrosyl iron complexes. In most Fe–S proteins, the terminal ligands on Fe are thiolate, but exceptions exist.

Octahedral clusters are inorganic or organometallic cluster compounds composed of six metals in an octahedral array. Many types of compounds are known, but all are synthetic.

Tetrahedral molecular geometry Central atom with four substituents located at the corners of a tetrahedron

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(−13) = 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.

Manganese heptoxide Chemical compound

Manganese(VII) oxide (manganese heptoxide) is an inorganic compound with the formula Mn2O7. This volatile liquid is highly reactive. It is a dangerous oxidizer and was first described in 1860. It is the acid anhydride of permanganic acid.

In chemistry, crystallography, and materials science, the coordination number, also called ligancy, of a central atom in a molecule or crystal is the number of atoms, molecules or ions bonded to it. The ion/molecule/atom surrounding the central ion/molecule/atom is called a ligand. This number is determined somewhat differently for molecules than for crystals.

High potential iron–sulfur protein

High potential iron-sulfur proteins (HIPIP) are a specific class of high-redox potential 4Fe-4S ferredoxins that functions in anaerobic electron transport and which occurs in photosynthetic bacteria and in Paracoccus denitrificans. The HiPIPs are small proteins which show significant variation in their sequences, their sizes, and in their oxidation- reduction potentials. As shown in the following schematic representation the iron-sulfur cluster is bound by four conserved cysteine residues.

 [ 4Fe-4S cluster]  | | | |  xxxxxxxxxxxxxxxxxxxCxCxxxxxxxCxxxxxCxxxx
Selenium tetrachloride Chemical compound

Selenium tetrachloride is the inorganic compound composed with the formula SeCl4. This compound exists as yellow to white volatile solid. It is one of two commonly available selenium chlorides, the other example being selenium monochloride, Se2Cl2. SeCl4 is used in the synthesis of other selenium compounds.

Octaazacubane Chemical compound

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.

Ferredoxin-thioredoxin reductase

Ferredoxin-thioredoxin reductase EC 1.8.7.2, systematic name ferredoxin:thioredoxin disulfide oxidoreductase, is a [4Fe-4S] protein that plays an important role in the ferredoxin/thioredoxin regulatory chain. It catalyzes the following reaction:

Lead(IV) chloride Chemical compound

Lead tetrachloride, also known as lead(IV) chloride, has the molecular formula PbCl4. It is a yellow, oily liquid which is stable below 0 °C, and decomposes at 50 °C. It has a tetrahedral configuration, with lead as the central atom. The Pb–Cl covalent bonds have been measured to be 247 pm and the bond energy is 243 kJ⋅mol−1.

A metallocarbohedryne is any one of a family of chemical compounds with the generic molecular formula M
8
C
12
, where M is a transition metal such as titanium, vanadium, zirconium, niobium, hafnium, molybdenum, chromium, or iron.

Metal cluster compound Cluster of three or more metals

Metal cluster compounds are a molecular ion or neutral compound composed of three or more metals and featuring significant metal-metal interactions.

Julia A. Kovacs is an American chemist specializing in bioinorganic chemistry. She is Professor of Chemistry at the University of Washington. Her research involves synthesizing small-molecule mimics of the active sites of metalloproteins, in order to investigate how cysteinates influence the function of non-heme iron enzymes, and the mechanism of the oxygen-evolving complex (OEC).

Das cubane Chemical compound

In coordination chemistry, the Das cubane is a transition metal carboxylate complex with the formula [CoO(OAc)py]4 where OAc is acetate and py is pyridine. The compound is named after Birinchi K. Das, who led the team that discovered the cluster. The compound features of Co4O4 core. Each Co(III) center is low-spin and has octahedral geometry. The compound is prepared by mixing a cobalt(II) salt with acetate and pyridine followed by oxidation with hydrogen peroxide.

References

  1. Perrin, Jr., B.S.; Ichive, T. (2013). "Identifying sequence determinants of reduction potentials of metalloproteins". Biological Inorganic Chemistry. 18 (6): 599–608. doi:10.1007/s00775-013-1004-6. PMC   3723707 . PMID   23690205.
  2. Lee, S. C.; Lo, W.; Holm, R. H., "Developments in the Biomimetic Chemistry of Cubane-Type and Higher Nuclearity Iron–Sulfur Clusters", Chem. Rev. 2014, doi : 10.1021/cr4004067
  3. Chakrabarty, Rajesh; Bora, Sanchay J.; Das, Birinchi K. (2007). "Synthesis, Structure, Spectral and Electrochemical Properties, and Catalytic Use of Cobalt(III)−Oxo Cubane Clusters". Inorganic Chemistry. 46 (22): 9450–9462. doi:10.1021/ic7011759. PMID   17910439.
  4. Umena, Yasufumi; Kawakami, Keisuke; Shen, Jian-Ren; Kamiya, Nobuo (2011). "Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å" (PDF). Nature. 473 (7345): 55–60. Bibcode:2011Natur.473...55U. doi:10.1038/nature09913. PMID   21499260. S2CID   205224374.
  5. Stey, Thomas; Stalke, Dietmar (2009). "Lead structures in lithium organic chemistry". PATAI'S Chemistry of Functional Groups. John Wiley & Sons, Ltd. doi:10.1002/9780470682531.pat0298. ISBN   9780470682531.
  6. Agrawal, Jai Prakash (2010). High Energy Materials: Propellants, Explosives and Pyrotechnics. Wiley-VCH. p. 498. ISBN   978-3-527-62880-3.