nitrogen-fixing bacteria

nitrogen-fixing bacteria

nitrogen-fixing bacteria: see nitrogen cycle.
Nitrogen is a chemical element that has the symbol N and atomic number 7 and atomic weight 14.0067. Elemental nitrogen is a colorless, odorless, tasteless and mostly inert diatomic gas at standard conditions, constituting 80% by volume of Earth's atmosphere.

Many industrially important compounds, such as ammonia, nitric acid, organic nitrates (propellants and explosives), and cyanides, contain nitrogen. The very strong bond in elemental nitrogen dominates nitrogen chemistry, causing difficulty for both organisms and industry in converting the into useful compounds, and releasing large amounts of energy when these compounds burn or decay back into nitrogen gas.

The element nitrogen was discovered by Daniel Rutherford, a Scottish physician in 1772. Nitrogen occurs in all living organisms—it is a constituent element of amino acids and thus of proteins, and of nucleic acids (DNA and RNA); resides in the chemical structure of almost all neurotransmitters; and is a defining component of alkaloids, biological molecules produced by many organisms.

History

Nitrogen (Latin nitrogenium, where nitrum (from Greek nitron) means "saltpetre" (see nitre), and genes means "forming") is formally considered to have been discovered by Daniel Rutherford in 1772, who called it noxious air or fixed air. That there was a fraction of air that did not support combustion was well known to the late 18th century chemist. Nitrogen was also studied at about the same time by Carl Wilhelm Scheele, Henry Cavendish, and Joseph Priestley, who referred to it as burnt air or phlogisticated air. Nitrogen gas was inert enough that Antoine Lavoisier referred to it as "mephetic air" or azote, from the Greek word αζωτος meaning "lifeless". Animals died in it, and it was the principal component of air in which animals had suffocated and flames had burned to extinction. Lavoisier's name for nitrogen still remains in the common names of many compounds, such as hydrazine and compounds of the azide ion. Compounds of nitrogen were known in the Middle Ages. The alchemists knew nitric acid as aqua fortis (strong water). The mixture of nitric and hydrochloric acids was known as aqua regia (royal water), celebrated for its ability to dissolve gold (the king of metals). The earliest military, industrial and agricultural applications of nitrogen compounds involved uses of saltpeter (sodium nitrate or potassium nitrate), notably in gunpowder, and much later, as fertilizer.

Properties

Nitrogen is a nonmetal, with an electronegativity of 3.0. It has five electrons in its outer shell and is therefore trivalent in most compounds. The triple bond in molecular nitrogen is one of the strongest in nature. The resulting difficulty of converting into other compounds, and the ease (and associated high energy release) of converting nitrogen compounds into elemental , have dominated the role of nitrogen in both nature and human economic activities.

At atmospheric pressure molecular nitrogen condenses (liquifies) at 77 K (−195.8 °C) and freezes at 63 K (−210.0 °C) into the beta hexagonal close-packed crystal allotropic form. Below 35.4 K (−237.6 °C) nitrogen assumes the alpha cubic crystal allotropic form. Liquid nitrogen, a fluid resembling water, but with 80.8% of the density, is a common cryogen.

Unstable allotropes of nitrogen consisting of more than two nitrogen atoms have been produced in the laboratory, like and . Under extremely high pressures (1.1 million atm) and high temperatures (2000 K), as produced under diamond anvil conditions, nitrogen polymerizes into the single bonded diamond crystal structure, an allotrope nicknamed "nitrogen diamond.

Isotopes

There are two stable isotopes of nitrogen: 14N and 15N. By far the most common is 14N (99.634%), which is produced in the CNO cycle in stars. Of the ten isotopes produced synthetically, 13N has a half life of ten minutes and the remaining isotopes have half lives on the order of seconds or less. Biologically-mediated reactions (e.g., assimilation, nitrification, and denitrification) strongly control nitrogen dynamics in the soil. These reactions typically result in 15N enrichment of the substrate and depletion of the product.

0.73% of the molecular nitrogen in Earth's atmosphere is comprised of the isotopologue 14N15N and almost all the rest is 14N2.

Electromagnetic spectrum

Molecular nitrogen (14N2) is largely transparent to infrared and visible radiation because it is a homonuclear molecule and thus has no dipole moment to couple to electromagnetic radiation at these wavelengths. Significant absorption occurs at extreme ultraviolet wavelengths, beginning around 100 nanometers. This is associated with electronic transitions in the molecule to states in which charge is not distributed evenly between nitrogen atoms. Nitrogen absorption leads to significant absorption of ultraviolet radiation in the Earth's upper atmosphere as well as in the atmospheres of other planetary bodies. For similar reasons, pure molecular nitrogen lasers typically emit light in the ultraviolet range.

Nitrogen also makes a contribution to visible air glow from the Earth's upper atmosphere, through electron impact excitation followed by emission. This visible blue air glow (seen in the polar aurora and in the re-entry glow of returning spacecraft) typically results not from molecular nitrogen, but rather from free nitrogen atoms combining with oxygen to form nitric oxide (NO).

Reactions

Nitrogen is generally unreactive at standard temperature and pressure. N2 reacts spontaneously with few reagents, being resilient to acids and bases as well as oxidants and most reductants. When nitrogen reacts spontaneously with a reagent, the net transformation is often called nitrogen fixation.

Nitrogen reacts with elemental lithium at STP. Lithium burns in an atmosphere of N2 to give lithium nitride:

6 Li + N2 → 2 Li3N
Magnesium also burns in nitrogen, forming magnesium nitride.
3 Mg + N2 → Mg3N2
N2 forms a variety of adducts with transition metals. The first example of a dinitrogen complex is [Ru(NH3)5(N2)]2+ (see figure at right). Such compounds are now numerous, other examples include IrCl(N2)(PPh3)2, W(N2)2(Ph2CH2CH2PPh2)2, and [(η5-C5Me4H)2Zr]2(μ2,η²,η²-N2). These complexes illustrate how N2 might bind to the metal(s) in nitrogenase and the catalyst for the Haber-Bosch Process. A catalytic process to reduce N2 to ammonia with the use of a molybdenum complex in the presence of a proton source was published in 2005. (see nitrogen fixation)

The starting point for industrial production of nitrogen compounds is the Haber-Bosch process, in which nitrogen is fixed by reacting and over a ferric oxide catalyst at about 500 °C and 200 atmospheres pressure. Biological nitrogen fixation in free-living cyanobacteria and in the root nodules of plants also produces ammonia from molecular nitrogen. The reaction, which is the source of the bulk of nitrogen in the biosphere, is catalysed by the nitrogenase enzyme complex which contains Fe and Mo atoms, using energy derived from hydrolysis of adenosine triphosphate (ATP) into adenosine diphosphate and inorganic phosphate (−20.5 kJ/mol).

Occurrence

Nitrogen is the largest single constituent of the Earth's atmosphere (78.082% by volume of dry air, 75.3% by weight in dry air). It is created by fusion processes in stars, and is estimated to be the 7th most abundant chemical element by mass in the universe.

Molecular nitrogen and nitrogen compounds have been detected in interstellar space by astronomers using the Far Ultraviolet Spectroscopic Explorer. Molecular nitrogen is a major constituent of the Saturnian moon Titan's thick atmosphere, and occurs in trace amounts in other planetary atmospheres.

Nitrogen is present in all living organisms in proteins, nucleic acids and other molecules. It typically makes up around 4% of the dry weight of plant matter, and around 3% of the weight of the human body. It is a large component of animal waste (for example, guano), usually in the form of urea, uric acid, ammonium compounds and derivatives of these nitrogenous products, which are essential nutrients for all plants that are unable to fix atmospheric nitrogen.

Nitrogen occurs naturally in a number of minerals, such as saltpetre (potassium nitrate), Chile saltpetre (sodium nitrate) and sal ammoniac (ammonium chloride). Most of these are relatively uncommon, partly because of the minerals' ready solubility in water. See also Nitrate minerals and Ammonium minerals.

Compounds

The main neutral hydride of nitrogen is ammonia (NH3), although hydrazine (N2H4) is also commonly used. Ammonia is more basic than water by 6 orders of magnitude. In solution ammonia forms the ammonium ion (NH4+). Liquid ammonia (b.p. 240 K) is amphiprotic (displaying either Brønsted-Lowry acidic or basic character) and forms ammonium and the less common amide ions (NH2-); both amides and nitride (N3-) salts are known, but decompose in water. Singly, doubly, triply and quadruply substituted alkyl compounds of ammonia are called amines (four substitutions, to form commercially and biologically important quarternary amines, results in a positively charged nitrogen, and thus a water-soluble, or at least amphiphilic, compound). Larger chains, rings and structures of nitrogen hydrides are also known, but are generally unstable. N22+ is another polyatomic cation as in hydrazine.

Other classes of nitrogen anions (negatively charged ions) are the poisonous azides (N3-), which are linear and isoelectronic to carbon dioxide, but which bind to important iron-containing enzymes in the body in a manner more resembling cyanide. Another molecule of the same structure is the colorless and relatively inert anesthetic gas dinitrogen monoxide , also known as laughing gas. This is one of a variety of oxides, the most prominent of which are nitrogen monoxide (NO) (known more commonly as nitric oxide in biology), a natural free radical molecule used by the body as a signal for short-term control of smooth muscle in the circulation. Another notable nitrogen oxide compound (a family often abbreviated NOx) is the reddish and poisonous nitrogen dioxide , which also contains an unpaired electron and is an important component of smog. Nitrogen molecules containing unpaired electrons show an understandable tendency to dimerize (thus pairing the electrons), and are generally highly reactive.

The more standard oxides, dinitrogen trioxide and dinitrogen pentoxide , are actually fairly unstable and explosive-- a tendency which is driven by the stability of as a product. The corresponding acids are nitrous and nitric acid , with the corresponding salts called nitrites and nitrates. Dinitrogen tetroxide (DTO) is one of the most important oxidisers of rocket fuels, used to oxidise hydrazine in the Titan rocket and in the recent NASA MESSENGER probe to Mercury. DTO is an intermediate in the manufacture of nitric acid , one of the few acids stronger than hydronium and a fairly strong oxidizing agent.

Nitrogen is notable for the range of explosively unstable compounds that it can produce. Nitrogen triiodide is an extremely sensitive contact explosive. Nitrocellulose, produced by nitration of cellulose with nitric acid, is also known as guncotton. Nitroglycerin, made by nitration of glycerin, is the dangerously unstable explosive ingredient of dynamite. The comparatively stable, but more powerful explosive trinitrotoluene (TNT) is the standard explosive against which the power of nuclear explosions are measured.

Nitrogen can also be found in organic compounds. Common nitrogen functional groups include: amines, amides, nitro groups, imines, and enamines. The amount of nitrogen in a chemical substance can be determined by the Kjeldahl method.

Applications

Nitrogen gas is acquired for industrial purposes by the fractional distillation of liquid air, or by mechanical means using gaseous air (i.e. pressurised reverse osmosis membrane or pressure swing adsorption). Commercial nitrogen is often a byproduct of air-processing for industrial concentration of oxygen for steelmaking and other purposes. When supplied compressed in cylinders it is often referred to as OFN (oxygen-free nitrogen).

Nitrogen gas has a wide variety of applications, including serving as an inert replacement for air where oxidation is undesirable;

Nitrogen molecules are less likely to escape from the inside of a tire compared with the traditional air mixture used. Air consists mostly of nitrogen and oxygen. Nitrogen molecules have a larger effective diameter than oxygen molecules and therefore diffuse through porous substances more slowly.

Molecular nitrogen, a diatomic gas, is apt to dimerize into a linear four nitrogen long polymer. This is an important phenomenon for understanding high-voltage nitrogen dielectric switches because the process of polymerization can continue to lengthen the molecule to still longer lengths in the presence of an intense electric field. A nitrogen polymer fog is thereby created. The second virial coefficient of nitrogen also shows this effect as the compressibility of nitrogen gas is changed by the dimerization process at moderate and low temperatures.

Nitrogen tanks are also replacing carbon dioxide as the main power source for paintball guns. The downside is that nitrogen must be kept at higher pressure than CO2, making N2 tanks heavier and more expensive.

Nitrogenated beer

A further example of its versatility is its use as a preferred alternative to carbon dioxide to pressurize kegs of some beers, particularly stouts and British ales, due to the smaller bubbles it produces, which make the dispensed beer smoother and headier. A modern application of a pressure sensitive nitrogen capsule known commonly as a "widget" now allows nitrogen charged beers to be packaged in cans and bottles.

Liquid nitrogen

Liquid nitrogen is a cryogenic liquid. At atmospheric pressure, it boils at −196.5 °C. When insulated in proper containers such as dewar flasks, it can be transported without much evaporative loss.

Like dry ice, the main use of liquid nitrogen is as a refrigerant. Among other things, it is used in the cryopreservation of blood, reproductive cells (sperm and egg), and other biological samples and materials. It is used in cold traps for certain laboratory equipment and to cool x-ray detectors. It has also been used to cool central processing units and other devices in computers which are overclocked, and which produce more heat than during normal operation.

Applications of nitrogen compounds

Molecular nitrogen (N2) in the atmosphere is relatively non-reactive due to its strong bond, and N2 plays an inert role in the human body, being neither produced or destroyed. In nature, nitrogen is converted into biologically (and industrially) useful compounds by lighting, and by some living organisms, notably certain bacteria (i.e. nitrogen fixing bacteria – see Biological role below). Molecular nitrogen is released into the atmosphere in the process of decay, in dead plant and animal tissues.

The ability to combine or fix molecular nitrogen is a key feature of modern industrial chemistry, where nitrogen and natural gas are converted into ammonia via the Haber process. Ammonia, in turn, can be used directly (primarily as a fertilizer, and in the synthesis of nitrated fertilizers), or as a precursor of many other important materials including explosives, largely via the production of nitric acid by the Ostwald process.

The organic and inorganic salts of nitric acid have been important historically as convenient stores of chemical energy. They include important compounds such as potassium nitrate (or saltpeter used in gunpowder) and ammonium nitrate, an important fertilizer and explosive (see ANFO). Various other nitrated organic compounds, such as nitroglycerin and trinitrotoluene, and nitrocellulose, are used as explosives and propellants for modern firearms. Nitric acid is used as an oxidizing agent in liquid fueled rockets. Hydrazine and hydrazine derivatives find use as rocket fuels and monopropellants. In most of these compounds, the basic instability and tendency to burn or explode is derived from the fact that nitrogen is present as an oxide, and not as the far more stable nitrogen molecule (N2) which is a product of the compounds' thermal decomposition. When nitrates burn or explode, the formation of the powerful triple bond in the N2 which results, produces most of the energy of the reaction.

Nitrogen is a constituent of molecules in every major drug class in pharmacology and medicine. Nitrous oxide (N2O) was discovered early in the 19th century to be a partial anesthetic, though it was not used as a surgical anesthetic until later. Called "laughing gas", it was found capable of inducing a state of social disinhibition resembling drunkenness. Other notable nitrogen-containing drugs are drugs derived from plant alkaloids, such as morphine (there exist many alkaloids known to have pharmacological effects; in some cases they appear natural chemical defences of plants against predation). Nitrogen containing drugs include all of the major classes of antibiotics, and organic nitrate drugs like nitroglycerin and nitroprusside which regulate blood pressure and heart action by mimicking the action of nitric oxide.

Biological role

Nitrogen is an essential part of amino acids and nucleic acids, both of which are essential to all life on Earth.

Molecular nitrogen in the atmosphere cannot be used directly by either plants or animals, and needs to be converted into nitrogen compounds, or "fixed," in order to be used by life. Precipitation often contains substantial quantities of ammonium and nitrate, both thought to be a result of nitrogen fixation by lightning and other atmospheric electric phenomena. However, because ammonium is preferentially retained by the forest canopy relative to atmospheric nitrate, most of the fixed nitrogen that reaches the soil surface under trees is in the form of nitrate. Soil nitrate is preferentially assimilated by tree roots relative to soil ammonium.

Specific bacteria (e.g. Rhizobium trifolium) possess nitrogenase enzymes which can fix atmospheric nitrogen (see nitrogen fixation) into a form (ammonium ion) which is chemically useful to higher organisms. This process requires a large amount of energy and anoxic conditions. Such bacteria may be free in the soil (e.g. Azotobacter) but normally exist in a symbiotic relationship in the root nodules of leguminous plants (e.g. clover, Trifolium species, or the soya bean plant, Glycine max). Nitrogen-fixing bacteria can be symbiotic with a number of unrelated plant species. Common examples are legumes, alders (Alnus) spp., lichens, Casuarina, Myrica, liverworts, and Gunnera.

As part of the symbiotic relationship, the plant subsequently converts the ammonium ion to nitrogen oxides and amino acids to form proteins and other biologically useful molecules, such as alkaloids. In return for the usable (fixed) nitrogen, the plant secretes sugars to the symbiotic bacteria.

Some plants are able to assimilate nitrogen directly in the form of nitrates which may be present in soil from natural mineral deposits, artificial fertilizers, animal waste, or organic decay (as the product of bacteria, but not bacteria specifically associated with the plant). Nitrates absorbed in this fashion are converted to nitrites by the enzyme nitrate reductase, and then converted to ammonia by another enzyme called nitrite reductase.

Nitrogen compounds are basic building blocks in animal biology. Animals use nitrogen-containing amino acids from plant sources, as starting materials for all nitrogen-compound animal biochemistry, including the manufacture of proteins and nucleic acids. Some plant-feeding insects are so dependent on nitrogen in their diet, that varying the amount of nitrogen fertilizer applied to a plant can affect the rate of reproduction of the insects feeding on it.

Soluble nitrate is an important limiting factor in the growth of certain bacteria in ocean waters. In many places in the world, artificial fertilizers applied to crop-lands to increase yields result in run-off delivery of soluble nitrogen to oceans at river mouths. This process can result in eutrophication of the water, as nitrogen-driven bacterial growth depletes water oxygen to the point that all higher organisms die. Well-known "dead zone" areas in the U.S. Gulf Coast and the Black Sea are due to this important polluting process.

Many saltwater fish manufacture large amounts of trimethylamine oxide to protect them from the high osmotic effects of their environment (conversion of this compound to dimethylamine is responsible for the early odor in unfresh saltwater fish: PMID 15186102). In animals, the free radical molecule nitric oxide (NO), which is derived from an amino acid, serves as an important regulatory molecule for circulation.

Animal metabolism of NO results in production of nitrite. Animal metabolism of nitrogen in proteins generally results in excretion of urea, while animal metabolism of nucleic acids results in excretion of urea and uric acid. The characteristic odor of animal flesh decay is caused by nitrogen-containing long-chain amines, such as putrescine and cadaverine.

Decay of organisms and their waste products may produce small amounts of nitrate, but most decay eventually returns nitrogen content to the atmosphere, as molecular nitrogen.

Safety

Rapid release of nitrogen gas into an enclosed space can displace oxygen, and therefore represents an asphyxiation hazard. This may happen with few warning symptoms, since the human carotid body is a relatively slow and a poor low-oxygen (hypoxia) sensing system. An example occurred shortly before the launch of the first Space Shuttle mission in 1981, when two technicians lost consciousness and died after they walked into a space located in the Shuttle's Mobile Launcher Platform that was pressurized with pure nitrogen as a precaution against fire. The technicians would have been able to exit the room if they had experienced early symptoms from nitrogen-breathing.

When inhaled at high partial pressures (more than about 4 bar, encountered at depths below about 30 m in scuba diving) nitrogen begins to act as an anesthetic agent. It can cause nitrogen narcosis, a temporary semi-anesthetized state of mental impairment similar to that caused by nitrous oxide.

Nitrogen also dissolves in the bloodstream and body fats. Rapid decompression (particularly in the case of divers ascending too quickly, or astronauts decompressing too quickly from cabin pressure to spacesuit pressure) can lead to a potentially fatal condition called decompression sickness (formerly known as caisson sickness or more commonly, the "bends"), when nitrogen bubbles form in the bloodstream, nerves, joints, and other sensitive or vital areas. Other "inert" gases (those gases other than carbon dioxide and oxygen) cause the same effects from bubbles composed of them, so replacement of nitrogen in breathing gases may prevent nitrogen narcosis, but does not prevent decompression sickness.

Direct skin contact with liquid nitrogen causes severe frostbite (cryogenic burns) within seconds, though not instantly on contact, depending on form of liquid nitrogen (liquid vs. mist) and surface area of the nitrogen-soaked material (soaked clothing or cotton causing more rapid damage than a spill of direct liquid to skin, which for a few seconds is protected by the Leidenfrost effect).

See also

References

Further reading

  • Garrett, Reginald H.; Grisham, Charles M. (1999). Biochemistry. 2nd edition, Fort Worth: Saunders College Publ..
  • Greenwood, Norman N.; Earnshaw, Alan (1984). Chemistry of the Elements. Oxford: Pergamon Press.
  • Nitrogen. Los Alamos National Laboratory. .

External links

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