A coordination complex consists of a central atom or ion, which is usually metallic and is called the coordination centre, and a surrounding array of bound molecules or ions, that are in turn known as ligands or complexing agents. Many metal-containing compounds, especially those that include transition metals, are coordination complexes.
In chemistry, a hypervalent molecule is a molecule that contains one or more main group elements apparently bearing more than eight electrons in their valence shells. Phosphorus pentachloride, sulfur hexafluoride, chlorine trifluoride, the chlorite ion, and the triiodide ion are examples of hypervalent molecules.
Valence shell electron pair repulsion (VSEPR) theory, is a model used in chemistry to predict the geometry of individual molecules from the number of electron pairs surrounding their central atoms. It is also named the Gillespie-Nyholm theory after its two main developers, Ronald Gillespie and Ronald Nyholm.
In chemistry, conformational isomerism is a form of stereoisomerism in which the isomers can be interconverted just by rotations about formally single bonds. While any two arrangements of atoms in a molecule that differ by rotation about single bonds can be referred to as different conformations, conformations that correspond to local minima on the potential energy surface are specifically called conformational isomers or conformers. Conformations that correspond to local maxima on the energy surface are the transition states between the local-minimum conformational isomers. Rotations about single bonds involve overcoming a rotational energy barrier to interconvert one conformer to another. If the energy barrier is low, there is free rotation and a sample of the compound exists as a rapidly equilibrating mixture of multiple conformers; if the energy barrier is high enough then there is restricted rotation, a molecule may exist for a relatively long time period as a stable rotational isomer or rotamer. When the time scale for interconversion is long enough for isolation of individual rotamers, the isomers are termed atropisomers. The ring-flip of substituted cyclohexanes constitutes another common form of conformational isomerism.
In chemistry, Van der Waals strain is strain resulting from Van der Waals repulsion when two substituents in a molecule approach each other with a distance less than the sum of their Van der Waals radii. Van der Waals strain is also called Van der Waals repulsion and is related to steric hindrance. One of the most common forms of this strain is eclipsing hydrogen, in alkanes.
In chemistry, a trigonal bipyramid formation is a molecular geometry with one atom at the center and 5 more atoms at the corners of a triangular bipyramid. This is one geometry for which the bond angles surrounding the central atom are not identical, because there is no geometrical arrangement with five terminal atoms in equivalent positions. Examples of this molecular geometry are phosphorus pentafluoride, and phosphorus pentachloride in the gas phase.
There are three series of binary phosphorus halides, containing phosphorus in the oxidation states +5, +3 and +2. All compounds have been described, in varying degrees of detail, although serious doubts have been cast on the existence of PI5. Mixed chalcogen halides also exist.
Iodine heptafluoride, also known as iodine(VII) fluoride or iodine fluoride, is an interhalogen compound with the chemical formula IF7. It has an unusual pentagonal bipyramidal structure, as predicted by VSEPR theory. The molecule can undergo a pseudorotational rearrangement called the Bartell mechanism, which is like the Berry mechanism but for a heptacoordinated system. It forms colourless crystals, which melt at 4.5 °C: the liquid range is extremely narrow, with the boiling point at 4.77 °C. The dense vapor has a mouldy, acrid odour. The molecule has D5h symmetry.
Xenon difluoride is a powerful fluorinating agent with the chemical formula XeF
2, and one of the most stable xenon compounds. Like most covalent inorganic fluorides it is moisture-sensitive. It decomposes on contact with water vapor, but is otherwise stable in storage. Xenon difluoride is a dense, colourless crystalline solid.
Sulfur tetrafluoride is the chemical compound with the formula SF4. It is a colorless corrosive gas that releases dangerous HF upon exposure to water or moisture. Despite these unwelcome characteristics, this compound is a useful reagent for the preparation of organofluorine compounds, some of which are important in the pharmaceutical and specialty chemical industries.
A pseudorotation is a set of intramolecular movements of attached groups (i.e., ligands) on a highly symmetric molecule, leading to a molecule indistinguishable from the initial one. The International Union of Pure and Applied Chemistry (IUPAC) defines a pseudorotation as a "[s]tereoisomerization resulting in a structure that appears to have been produced by rotation of the entire initial molecule", the result of which is a "product" that is "superposable on the initial one, unless different positions are distinguished by substitution, including isotopic substitution." Well known examples are the intramolecular isomerization of trigonal bipyramidal compounds by the Berry pseudorotation mechanism, and the out-of-plane motions of carbon atoms exhibited by cyclopentane, leading to the interconversions it experiences between its many possible conformers (envelope, twist). Note, no angular momentum is generated by this motion. In these and related examples, a small displacement of the atomic positions leads to a loss of symmetry until the symmetric product re-forms (see image example below), where these displacements are typically along low-energy pathways. The Berry mechanism refers to the facile interconversion of axial and equatorial ligand in MX5 types of compounds, e.g. D3h-symmetric PF5 (shown). Finally, in a formal sense, the term pseudorotation is intended to refer exclusively to dynamics in symmetrical molecules, though mechanisms of the same type are invoked for lower symmetry molecules as well.
Fluxional molecules are molecules that undergo dynamics such that some or all of their atoms interchange between symmetry-equivalent positions. Because virtually all molecules are fluxional in some respects, e.g. bond rotations in most organic compounds, the term fluxional depends on the context and the method used to assess the dynamics. Often, a molecule is considered fluxional if its spectroscopic signature exhibits line-broadening due to chemical exchange. In some cases, where the rates are slow, fluxionality is not detected spectroscopically, but by isotopic labeling and other methods.
Phosphorus pentafluoride, PF5, is a phosphorus halide. It is a colourless, toxic gas that fumes in air.
The Ray–Dutt twist is a mechanism proposed for the racemization of octahedral complexes containing three bidentate chelate rings. Such complexes typically adopt an octahedral molecular geometry in their ground states, in which case they possess helical chirality. The pathway entails formation of an intermediate of C2v point group symmetry. An alternative pathway that also does not break any metal-ligand bonds is called the Bailar twist. Both of these mechanism product complexes wherein the ligating atoms are arranged in an approximate trigonal prism.
In molecular geometry, square pyramidal geometry describes the shape of certain compounds with the formula ML5 where L is a ligand. If the ligand atoms were connected, the resulting shape would be that of a pyramid with a square base. The point group symmetry involved is of type C4v. The geometry is common for certain main group compounds that have a stereochemically active lone pair, as described by VSEPR theory. Certain compounds crystallize in both the trigonal bipyramidal and the square pyramidal structures, notably [Ni(CN)5]3−.
Disphenoidal or Seesaw (also known as Sawhorse is a type of molecular geometry where there are four bonds to a central atom with overall C2v molecular symmetry. The name "seesaw" comes from the observation that it looks like a playground seesaw. Most commonly, four bonds to a central atom result in tetrahedral or, less commonly, square planar geometry.
In chemistry, T-shaped molecular geometry describes the structures of some molecules where a central atom has three ligands. Ordinarily, three-coordinated compounds adopt trigonal planar or pyramidal geometries. Examples of T-shaped molecules are the halogen trifluorides, such as ClF3.
The Bartell mechanism is a pseudorotational mechanism similar to the Berry mechanism. It occurs only in molecules with a pentagonal bipyramidal molecular geometry, such as IF7. This mechanism was first predicted by H. B. Bartell. The mechanism exchanges the axial atoms with one pair of the equatorial atoms with an energy requirement of about 2.7 kcal/mol. Similarly to the Berry mechanism in square planar molecules, the symmetry of the intermediary phase of the vibrational mode is "chimeric" of other mechanisms; it displays characteristics of the Berry mechanism, a "lever" mechanism seen in pseudorotation of disphenoidal molecules, and a "turnstile" mechanism (which can be seen in trigonal bipyramidal molecules under certain conditions).
Phosphorus trifluorodichloride is a chemical compound with the chemical formula PF3Cl2. The covalent molecule trigonal bipyramidal molecular geometry. The central phosphorus atom has sp3d hybridization, and the molecule has an asymmetric charge distribution. It appears as a colorless gas with a disagreeable odor which turns to a liquid at -8 °C.
Tetradentate ligands are ligands that bind four donor atoms to a central atom to form a coordination complex. This number of donor atoms that bind is called denticity and is a way to classify ligands. Tetradentate ligands are common in nature in the form of chlorophyll which has a core ligand called chlorin, and heme with a core ligand called porphyrin. They add much of the colour seen in plants and humans. Phthalocyanine is an artificial macrocyclic tetradentate ligand that is used to make blue and green pigments.
