A clathrate, clathrate compound or cage compound is a chemical substance consisting of a lattice of one type of molecule trapping and containing a second type of molecule. The name clathrate complex used to refer only to the inclusion complex of hydroquinone, but recently it has been adopted for many other weak composites which consist of a host molecule (forming the basic frame) and a guest molecule (held in the host molecule by inter-molecular interaction). Clathrates are also called host-guest complexes, inclusion compounds, adducts (chiefly in the case of urea and thiourea) and, in the oil industry, hydrates. They used to be called molecular compounds.
A clathrate hydrate, in particular, is a special type of gas hydrate in which a lattice of water molecules encloses molecules of a trapped gas. Large amounts of methane naturally frozen in this form have been discovered both in permafrost formations and under the ocean sea-bed.[1] Researchers have begun to investigate silicon and germanium clathrates for possible semiconducting, superconducting, and thermoelectric properties.
The word clathrate is derived from the Latin clatratus meaning with bars or a lattice.[2]
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History
The history of clathrate compounds is relatively recent. Clathrate hydrates were discovered in 1810 by Humphry Davy.[3] Clathrates were studied by P. Pfeiffer in 1927 and in 1930, E. Hertel defined "molecular compounds" as substances decomposed into individual components following the mass action law in solution or gas state. In 1945, H. M. Powell analyzed the crystal structure of these compounds and named them clathrates.
Urea- and thiourea-hosted clathrates were applied to the separation of paraffin. Thereafter, cyclodextrin, crown ether, and cryptand were found as host molecules (see figure). A much studied host molecule is Dianin's compound.
Properties
Clathrate complexes are various and include, for example, strong interaction via chemical bonds between host molecules and guest molecules, or guest molecules set in the geometrical space of host molecules by weak intermolecular force. Typical examples of host-guest complexes are inclusion compounds and intercalation compounds.
Clathrates can be isolated as chemically different species, and may have structural and positional isomers (enantiomers and diastereomers).
Photorelease technology
Photolytically-sensitive caged compounds are a particularly useful resource for the biologist who wishes to intervene in cellular processes in a specific and targeted manner. Biomolecules ranging from the size of protons to proteins have been encapsulated and utilized. Neurotransmitters such as glutamate and GABA, small molecules such as ATP and IP3, ions such as Ca2+, proteins such as actin and PKA, DNA, and mRNA have all been successfully caged. When the compound is irradiated, the compound of interest is liberated from the cage. The use of caged compounds, compared to other methods of biological intervention, allows for much greater spatial and temporal targeting.
When it comes to the synthesis of caged compounds, several considerations must be taken into mind. The caged compound must be biologically inert. The rate of uncaging must be faster than the process it is intervening in. The uncaging must also be efficient, since excess UV or infrared light irradiation may disrupt other cellular processes. The compounds must be sufficiently water soluble and hydrolytically stable, so as to not be cleaved by hydrolysis. Different compounds fare with these variables in different ways.
Liberation of the caged compound can be via flash lamps, UV lasers, or two-photon excitation microscopy. Flash lamps are cheap and efficient, but the amount of liberated compound is difficult to quantify. UV lasers are more expensive, but allow for more precise quantification. Two-photon excitation is the more targeted method of irradiation, as it allows for three-dimensional localization.
Caged compounds are applied either intracellularly by methods such as patch pipette or microinjection or extracellularly by bathing cells of interest in the solution or picospritzer.
The amount of compound released can be quantified in various ways. Proteins can be synthesized that alter their fluorescence emission upon binding to substrates. Dyes may be used to quantify calcium ions. For protons and proton-released compounds, amount may be quantified by measuring pH. For compounds that cannot be quantified using any of these methods, one must resort to the crude tactic of estimating amount as a function of flux density and quantum yield. [4]
Media references
- In John Barnes' science-fiction novel Mother of Storms, the destruction of Arctic sea bed clathrates and the subsequent release of trapped CO2 and methane is central to the plot development involving a vast supersonic hurricane.
- During the Deepwater Horizon oil spill clathrate formation inside a large device intended to cap the main leak prevented its successful deployment.[5]
- In the massively multiplayer online game Eve Online, strontium clathrates, mined from ice asteroids, have various strategic applications.
See also
- Clathrate gun hypothesis, a hypothesis regarding the sudden release of methane clathrate from ocean sediments.
- Weaire-Phelan structure, related to clathrate structure.
- Chelate
References
- ^ Pearce, Fred (27 June 2009). "Ice on fire: The next fossil fuel". New Scientist. pp. 30–33. http://www.newscientist.com/search?doSearch=true&query=clathrates. Retrieved 2009-07-05.
- ^ Latin dictionary
- ^ Ellen Thomas (11 2004). "Clathrates: little known components of the global carbon cycle". Wesleyan University. http://ethomas.web.wesleyan.edu/ees123/clathrate.htm. Retrieved 13 December 2007.
- ^ Ellis-Davies, Graham C. R. (July 2007). "Caged compounds: photorelease technology for control of cellular chemistry and physiology". Nature Methods. http://www.nature.com/nmeth/journal/v4/n8/full/nmeth1072.html.
- ^ John Timmer (05 2010). "Frozen methane, from the gulf oil spill to climate change". Ars Technica. http://arstechnica.com/science/news/2010/05/frozen-methane-from-the-gulf-oil-spill-to-climate-change.ars. Retrieved 16 May 2010.