Cubane-type Cluster on:
[Wikipedia]
[Google]
[Amazon]
A cubane-type cluster is an arrangement of atoms in a
DasCubane.png, Das cubane, oO(OAc)pysub>4 (OAc =
Several
A cubane-type cluster is an arrangement of atoms in a molecular structure
Molecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that deter ...
that forms a cube
In geometry, a cube is a three-dimensional solid object bounded by six square faces, facets or sides, with three meeting at each vertex. Viewed from a corner it is a hexagon and its net is usually depicted as a cross.
The cube is the only r ...
. In the idealized case, the eight vertices are symmetry equivalent and the species has Oh symmetry
Symmetry (from grc, συμμετρία "agreement in dimensions, due proportion, arrangement") in everyday language refers to a sense of harmonious and beautiful proportion and balance. In mathematics, "symmetry" has a more precise definit ...
. Such a structure is illustrated by the hydrocarbon
In organic chemistry, a hydrocarbon is an organic compound consisting entirely of hydrogen and carbon. Hydrocarbons are examples of group 14 hydrides. Hydrocarbons are generally colourless and hydrophobic, and their odors are usually weak or ex ...
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 an ...
. With chemical formula
In chemistry, a chemical formula is a way of presenting information about the chemical proportions of atoms that constitute a particular chemical compound or molecule, using chemical element symbols, numbers, and sometimes also other symbols, ...
, cubane has carbon atoms at the corners of a cube and covalent bond
A covalent bond is a chemical bond that involves the sharing of electrons to form electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs. The stable balance of attractive and repulsive forces between atoms ...
s forming the edges. Most cubanes have more complicated structures, usually with nonequivalent vertices. They may be simple covalent compounds or macromolecular
A macromolecule is a very large molecule important to biophysical processes, such as a protein or nucleic acid. It is composed of thousands of covalently bonded atoms. Many macromolecules are polymers of smaller molecules called monomers. The ...
or supramolecular cluster compound
In chemistry, an atom cluster (or simply 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' ...
s.
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 includeselenium tetrachloride
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, S ...
, tellurium tetrachloride
Tellurium tetrachloride is the inorganic compound with the empirical formula TeCl4. The compound is volatile, subliming at 200 °C at 0.1 mmHg. Molten TeCl4 is ionic, dissociating into TeCl3+ and Te2Cl102−.
Structure
TeCl4 is mon ...
, and sodium silox.
Cubane clusters are common throughout bioinorganic chemistry
Bioinorganic chemistry is a field that examines the role of metals in biology. Bioinorganic chemistry includes the study of both natural phenomena such as the behavior of metalloproteins as well as artificially introduced metals, including those t ...
. Ferredoxin
Ferredoxins (from Latin ''ferrum'': iron + redox, often abbreviated "fd") 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 t ...
s containing e4S4iron–sulfur cluster
Iron–sulfur clusters (or iron–sulphur clusters in British spelling) 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 are pervasive in nature. 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
Cysteine (symbol Cys or C; ) is a semiessential proteinogenic amino acid with the formula . The thiol side chain in cysteine often participates in enzymatic reactions as a nucleophile.
When present as a deprotonated catalytic residue, sometime ...
residues. In this way, each Fe center achieves 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 ...
. Some e4S4clusters arise via dimerization of square-shaped e2S2precursors. Many synthetic analogues are known including heterometallic derivatives.
acetate
An acetate is a salt (chemistry), salt formed by the combination of acetic acid with a base (e.g. Alkali metal, alkaline, Alkaline earth metal, earthy, Transition metal, metallic, nonmetallic or radical Radical (chemistry), base). "Acetate" als ...
; py = pyridine
Pyridine is a basic heterocyclic organic compound with the chemical formula . It is structurally related to benzene, with one methine group replaced by a nitrogen atom. It is a highly flammable, weakly alkaline, water-miscible liquid with a d ...
)
Fe4S4.svg, Ferredoxin (4Fe-4S-cubane)
Oxygen Evolving Complex Crystal structure to 1.9 Angstrom Resolution.png, CaMn3O4 cubane in 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 ...
.
Cubane-3D-balls.png, 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 an ...
, C8H8
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 ...
compounds exist as clusters in solution, typically 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 ...
s, with the formula Lisub>4. Examples include 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 so ...
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.
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 cl ...
is a hypothetical allotrope of 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 se ...
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
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 ...
at the corners, and it also does not enjoy the kinetic stability
In chemistry and physics, metastability denotes an intermediate energetic state within a dynamical system other than the system's state of least energy.
A ball resting in a hollow on a slope is a simple example of metastability. If the ball i ...
seen for its organic analogues.
References
{{Reflist Molecular geometry