Bromine

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From Wikipedia, the free encyclopedia

Bromine,  ₃₅Br

General properties
Name, symbol	bromine, Br
Pronunciation	/ˈbroʊmiːn/ or /ˈbroʊmɨn/ BROH-meen or BROH-min
Appearance	gas/liquid: red-brown solid: metallic luster
Bromine in the periodic table
Cl ↑ Br ↓ I selenium ← bromine → krypton
Atomic number	35
Standard atomic weight	79.904[1] (79.901–79.907)[2]
Element category	diatomic nonmetal
Group, block	group 17 (halogens), p-block
Period	period 4
Electron configuration	[Ar] 3d10 4s2 4p5
per shell	2, 8, 18, 7
Physical properties
Phase	liquid
Melting point	265.8 K ​(−7.2 °C, ​19 °F)
Boiling point	332.0 K ​(58.8 °C, ​137.8 °F)
Density near r.t.	Br2, liquid: 3.1028 g·cm−3
Triple point	265.90 K, ​5.8 kPa[3]
Critical point	588 K, 10.34 MPa[3]
Heat of fusion	(Br2) 10.571 kJ·mol−1
Heat of vaporization	(Br2) 29.96 kJ·mol−1
Molar heat capacity	(Br2) 75.69 J·mol−1·K−1
vapor pressure P (Pa) 1 10 100 1 k 10 k 100 k at T (K) 185 201 220 244 276 332
Atomic properties
Oxidation states	7, 5, 4, 3, 1, −1 ​(a strongly acidic oxide)
Electronegativity	Pauling scale: 2.96
Ionization energies	1st: 1139.9 kJ·mol−1 2nd: 2103 kJ·mol−1 3rd: 3470 kJ·mol−1
Atomic radius	empirical: 120 pm
Covalent radius	120±3 pm
Van der Waals radius	185 pm
Miscellanea
Crystal structure	​orthorhombic
Speed of sound	206 m·s−1 (at 20 °C)
Thermal conductivity	0.122 W·m−1·K−1
Electrical resistivity	7.8×1010 Ω·m (at 20 °C)
Magnetic ordering	diamagnetic[4]
CAS Registry Number	7726-95-6
History
Discovery and first isolation	Antoine Jérôme Balard and Leopold Gmelin (1825)
Most stable isotopes
Main article: Isotopes of bromine
iso NA half-life DM DE (MeV) DP 79Br 50.69% 79Br is stable with 44 neutrons 81Br 49.31% 81Br is stable with 46 neutrons

Bromine (from Greek: βρῶμος, brómos, meaning "strong-smelling" or "stench")^[5] is a chemical element with symbol Br, and atomic number 35. It is a halogen. The element was isolated independently by two chemists, Carl Jacob Löwig and Antoine Jerome Balard, in 1825–1826. Elemental bromine is a fuming red-brown liquid at room temperature, corrosive and toxic, with properties between those of chlorine and iodine. Free bromine does not occur in nature, but occurs as colorless soluble crystalline mineral halide salts, analogous to table salt.

Bromine is rarer than about three-quarters of elements in the Earth's crust. The high solubility of bromide ions has caused its accumulation in the oceans, and commercially the element is easily extracted from brine pools, mostly in the United States, Israel and China. About 556,000 tonnes were produced in 2007, an amount similar to the far more abundant element magnesium.^[6]

At high temperatures, organobromine compounds readily convert to free bromine atoms, a process which has the effect of stopping free radical chemical chain reactions. This effect makes organobromine compounds useful as fire retardants; more than half the bromine produced industrially worldwide each year is put to this use. Unfortunately, the same property causes sunlight to convert volatile organobromine compounds to free bromine atoms in the atmosphere, and an unwanted side effect of this process is ozone depletion. As a result, many organobromide compounds that were formerly in common use—such as the pesticide, methyl bromide—have been abandoned. Bromine compounds are still used for purposes such as in well drilling fluids, in photographic film, and as an intermediate in the manufacture of organic chemicals.

Bromine has been long believed to have no essential function in mammals, but recent research suggests that bromine is necessary for tissue development. In addition, bromine is used preferentially over chlorine by one antiparasitic enzyme in the human immune system. Organobromides are needed and produced enzymatically from bromide by some lower life forms in the sea, particularly algae, and the ash of seaweed was one source of bromine's discovery. As a pharmaceutical, the simple bromide ion, Br⁻, has inhibitory effects on the central nervous system, and bromide salts were once a major medical sedative, before being replaced by shorter-acting drugs. They retain niche uses as antiepileptics.

§Characteristics

§Physical

Illustrative and secure bromine sample for teaching

The element bromine exists as a diatomic molecule, Br₂. It is a dense, mobile, slightly transparent reddish-brown liquid, that evaporates easily at standard temperature and pressures to give an orange vapor (its color resembles nitrogen dioxide) that has a strongly disagreeable odor resembling that of chlorine. It is one of only two elements on the periodic table that are known to be liquids at room temperature (mercury is the other, although caesium, gallium, and rubidium melt just above room temperature).

At a pressure of 55 GPa (roughly 540,000 times atmospheric pressure) bromine converts to a metal. At 75 GPa it converts to a face centered orthorhombic structure. At 100 GPa it converts to a body centered orthorhombic monatomic form.^[7]

§Chemical

Being less reactive than chlorine but more reactive than iodine, bromine reacts vigorously with metals, especially in the presence of water, to give bromide salts. It is also reactive toward most organic compounds, especially upon illumination, conditions that favor the dissociation of the diatomic molecule into bromine radicals:

Br₂ 2 Br·

It bonds easily with many elements and has a strong bleaching action.

Bromine is slightly soluble in water, but it is highly soluble in organic solvents such as carbon disulfide, carbon tetrachloride, aliphatic alcohols, and acetic acid.

§Isotopes[edit]

Bromine has two stable isotopes, ⁷⁹Br (50.69%) and ⁸¹Br (49.31%). At least 23 radioisotopes are known. Many of the bromine isotopes are fission products. Several of the heavier bromine isotopes from fission are delayed neutron emitters, important to the controllability of a nuclear reactor. All of the radioactive bromine isotopes are relatively short lived. The longest half-life is the neutron deficient ⁷⁷Br at 2.376 days. The longest half-life on the neutron rich side is ⁸²Br at 1.471 days. A number of the bromine isotopes exhibit metastable isomers. Stable ⁷⁹Br exhibits a radioactive isomer, with a half-life of 4.86 seconds. It decays by isomeric transition to the stable ground state.^[8]The isotopes of bromine range from ⁶⁷Br to ⁹⁸Br. One of these, ⁶⁷Br has an unknown half life. Six isotopes, ⁹⁵Br to ⁹⁸Br, ⁶⁸Br, and ⁶⁹Br have half-lives under a microsecond. The isotopes ⁹¹Br to ⁹⁴Br and ⁷⁰Br have half lives of a microsecond to a second. All but two of the remaining isotopes of bromine have half lives of 1 second to 10,000,000 seconds. The other two, ⁷⁹Br and ⁸¹Br, are stable.^[9]

The three lightest isotopes of bromine (⁶⁷Br to ⁶⁹Br) decay via proton emission. The isotopes ⁷⁰Br through ⁷⁸Br decay via electron capture or positron emission. ⁸⁰Br and ⁸²Br to ⁹⁷Br decay via electron emission. ⁹⁸Br decays via neutron emission.^[10]

§History

Bromine was discovered independently by two chemists, Carl Jacob Löwig^[11] and Antoine Balard,^[12][13] in 1825 and 1826, respectively.^[14]

Balard found bromine chemicals in the ash of seaweed from the salt marshes of Montpellier. The seaweed was used to produce iodine, but also contained bromine. Balard distilled the bromine from a solution of seaweed ash saturated with chlorine. The properties of the resulting substance resembled that of an intermediate of chlorine and iodine; with those results he tried to prove that the substance was iodine monochloride (ICl), but after failing to do so he was sure that he had found a new element and named it muride, derived from the Latin word muria for brine.^[13]

Löwig isolated bromine from a mineral water spring from his hometown Bad Kreuznach in 1825. Löwig used a solution of the mineral salt saturated with chlorine and extracted the bromine with diethyl ether. After evaporation of the ether a brown liquid remained. With this liquid as a sample for his work he applied for a position in the laboratory of Leopold Gmelin in Heidelberg. The publication of the results was delayed and Balard published his results first.^[15]

After the French chemists Louis Nicolas Vauquelin, Louis Jacques Thénard, and Joseph-Louis Gay-Lussac approved the experiments of the young pharmacist Balard, the results were presented at a lecture of the Académie des Sciences and published in Annales de Chimie et Physique.^[12] In his publication Balard states that he changed the name from muride to brôme on the proposal of M. Anglada. (Brôme (bromine) derives from the Greek βρωμος (stench).^[12][16]) Other sources claim that the French chemist and physicist Joseph-Louis Gay-Lussac suggested the name brôme for the characteristic smell of the vapors.^[17][18] Bromine was not produced in large quantities until 1860.

The first commercial use, besides some minor medical applications, was the use of bromine for the daguerreotype. In 1840 it was discovered that bromine had some advantages over the previously used iodine vapor to create the light sensitive silver halide layer used for daguerreotypy.^[19]

Potassium bromide and sodium bromide were used as anticonvulsants and sedatives in the late 19th and early 20th centuries, until they were gradually superseded by chloral hydrate and then the barbiturates.^[20] In the early years of the First World War, bromine compounds such as xylyl bromide were used as poison gas.^[21]

§Occurrence

World bromine production trend

View of salt evaporation pans on the Dead Sea, where Jordan (right) and Israel (left) produce salt and bromine

 WikiMiniAtlas

31°9′0″N 35°27′0″E / 31.15000°N 35.45000°E / 31.15000; 35.45000

The diatomic element Br₂ does not occur naturally. Instead, bromine exists exclusively as bromide salts in diffuse amounts in crustal rock. Owing to leaching, bromide salts have accumulated in sea water at 65 parts per million (ppm),^[22] which is less than chloride. Bromine may be economically recovered from bromide-rich brine wells and from the Dead Sea waters (up to 50,000 ppm).^[23][24] It exists in the Earth's crust at an average concentration of 0.4 ppm, making it the 62nd most abundant element. The bromine concentration in soils varies normally between 5 and 40 ppm, but some volcanic soils can contain up to 500 ppm. The concentration of bromine in the atmosphere is extremely low, at only a few ppt.^[25] A large number of organobromine compounds are found in small amounts in nature.

China's bromine reserves are located in the Shandong Province and Israel's bromine reserves are contained in the waters of the Dead Sea.^[26] The largest bromine reserve in the United States is located in Columbia County and Union County, Arkansas, U.S.^[27]

§Production

Bromine production has increased sixfold since the 1960s. Approximately 556,000 tonnes (worth around US $2.5 billion) were produced in 2007 worldwide, with the predominant contribution from the United States (226,000 t) and Israel (210,000 t).^[6][25][28] US production was excluded from the United States Geological Survey after 2007, and from the 380,000 tonnes mined by other countries in 2010, 140,000 t were produced by China, 130,000 t by Israel and 80,000 t by Jordan.^[29]

Bromide-rich brines are treated with chlorine gas, flushing through with air. In this treatment, bromide anions are oxidized to bromine by the chlorine gas.

2 Br⁻ + Cl₂ → 2 Cl⁻ + Br₂

§Laboratory methods of production

In the laboratory, because of its commercial availability and long shelf-life, bromine is not typically prepared. Small amounts of bromine can however be generated through the reaction of solid sodium bromide with concentrated sulfuric acid (H₂SO₄). The first stage is formation of hydrogen bromide (HBr), which is a gas, but under the reaction conditions some of the HBr is oxidized further by the sulfuric acid to form bromine (Br₂) and sulfur dioxide (SO₂).

NaBr (s) + H₂SO₄ (aq) → HBr (aq) + NaHSO₄ (aq)

2 HBr (aq) + H₂SO₄ (aq) → Br₂ (g) + SO₂ (g) + 2 H₂O (l)

Non oxidizing acid alternatives, such as the use of dilute hydrobromic acid with sodium hypobromite, are also available, as the hypobromous acid formed from them is unstable in the presence of bromide, being reduced by it according to the reaction:

2 OBr⁻ (aq) + 4 HBr (aq) → 2Br₂ + 2H₂O + 2Br⁻

The reactions are the reverse of disproportionation reactions of elemental bromine in base, and are called comproportionation. A similar reaction happens with sodium hypochlorite, acid, and chloride, leading to elemental chlorine.

Reactions involving an oxidizing agent, such as potassium permanganate or manganese dioxide, on bromide ions in the presence of an acid, also give bromine in the reactions analogous to the formation of elemental chlorine and iodine from an acid and oxidant.

Like iodine, bromine is soluble in chloroform but only slightly soluble in water. In water, the solubility can be increased by the presence of bromide ions. Concentrated solutions of bromine are rarely prepared in the lab because of hazards. As is the case with chlorine solutions or iodine solutions, sodium thiosulphate (or any soluble thiosulphate) is an effective reagent for reducing bromine to colorless odorless bromide, thus dealing with stains and odor from the element in unwanted places. For the same reason, thiosulfate ("fixer's hypo") is used in photography to deal with free bromine in silver bromide film emulsions.

§Compounds and chemistry

§Organic chemistry

N-Bromosuccinimide

As with other halogens, bromine substitutes for hydrogen in hydrocarbons, bonding covalently to carbon. As with other halogens, the C-Br product of this substitution is generally colorless if the corresponding C-H compound is colorless. Addition of covalently bonded bromine tends to increase the density and raise the melting point of organic compounds.

Organic compounds are brominated by either addition or substitution reactions. Bromine undergoes electrophilic addition to the double-bonds of alkenes, via a cyclic bromonium intermediate. In non-aqueous solvents such as carbon disulfide, this yields the di-bromo product. For example, reaction with ethylene will produce 1,2-dibromoethane. Bromine also undergoes electrophilic substitution to phenols and anilines. When used as bromine water, a small amount of the corresponding bromohydrin is formed as well as the dibromo compound. So reliable is the reactivity of bromine that bromine water is employed as a reagent to test for the presence of alkenes, phenols, and anilines. Like the other halogens, bromine participates in free radical reactions. For example, hydrocarbons are brominated upon treatment with bromine in the presence of light.

Bromine, sometimes with a catalytic amount of phosphorus, easily brominates carboxylic acids at the α-position. This method, the Hell-Volhard-Zelinsky reaction, is the basis of the commercial route to bromoacetic acid. N-Bromosuccinimide is commonly used as a substitute for elemental bromine, being easier to handle, and reacting more mildly and thus more selectively. Organic bromides are often preferable relative to the less reactive chlorides and more expensive iodide-containing reagents. Thus, Grignard and organolithium compound are most often generated from the corresponding bromides.

Certain bromine-related compounds have been evaluated to have an ozone depletion potential or bioaccumulate in living organisms. As a result, many industrial bromine compounds are no longer manufactured, are being restricted, or scheduled for phasing out. The Montreal Protocol mentions several organobromine compounds for this phase out.

§Inorganic chemistry

Inorganic bromine compounds adopt a variety of oxidation states from −1 to +7.^[30] In nature, bromide (Br⁻) is by far the most common state, and departures from this -1 oxidation state are entirely due to living organisms and bromide's interaction with biologically produced oxidants, such as free oxygen.
Like other halogens, bromide ion is colorless, and forms a number of transparent ionic mineral salts, analogous to chloride. Bromide ion is highly soluble in water.

Examples of compounds for bromine's various oxidation states are shown below:

Oxidation states of bromine
−1	HBr
0	Br 2
+1	BrCl
+3	BrF 3
+5	BrF 5
+5	BrO− 3
+7	BrO− 4

Bromine is an oxidizer, and it will oxidize iodide ions to iodine, being itself reduced to bromide:

Br₂ + 2 I⁻ → 2 Br⁻ + I₂

Bromine will also oxidize metals and metalloids to the corresponding bromides. Anhydrous bromine is less reactive toward many metals than hydrated bromine, however. Dry bromine reacts vigorously with aluminium, titanium, mercury as well as alkaline earths and alkali metals.
Dissolving bromine in alkaline solution gives a mixture of bromide and hypobromite:

Br₂ + 2 OH⁻ → Br⁻ + OBr⁻ + H₂O

This hypobromite is responsible for the bleaching abilities of bromide solutions. Warming of these solutions causes the disproportion reaction of the hypobromite to give bromate, a strong oxidising agent very similar to chlorate.

3 BrO− → BrO−
3 + 2 Br−

In contrast to the route to perchlorates, perbromates are not accessible through electrolysis but only by reacting bromate solutions with fluorine or ozone.

BrO₃⁻ + H₂O + F₂ → BrO−
4 + 2 HF

BrO₃⁻ + O₃ → BrO−
4 + O₂

Bromine reacts violently and explosively with aluminium metal, forming aluminium bromide:

2 Al + 3 Br₂ → 2 AlBr₃

Bromine reacts with hydrogen in gaseous form and gives hydrogen bromide:

H₂ + Br₂ → 2HBr

Bromine reacts with alkali metal iodides in a displacement reaction. This reaction forms alkali metal bromides and produces elemental iodine:

2 NaI + Br₂ → 2 NaBr + I₂

2 KI + Br₂ → 2 KBr + I₂

§Applications

A wide variety of organobromine compounds are used in industry. Some are prepared from bromine and others are prepared from hydrogen bromide, which is obtained by burning hydrogen in bromine.^[31]

Illustrative of the addition reaction^[32] is the preparation of 1,2-dibromoethane, the organobromine compound produced in the largest amounts:

C₂H₄ + Br₂ → CH₂BrCH₂Br

§Flame retardant

Tetrabromobisphenol A

Brominated flame retardants represent a commodity of growing importance, and represent the largest commercial use of bromine. When the brominated material burns, the flame retardant produces hydrobromic acid which interferes in the radical chain reaction of the oxidation reaction of the fire. The mechanism is that the highly reactive hydrogen radicals, oxygen radicals, and hydroxy radicals react with hydrobromic acid to form less reactive bromine radicals (i.e., free bromine atoms). Bromine atoms may also react directly with other radicals to help terminate the free radical chain-reactions that characterize combustion.^[33][34]

To make brominated polymers and plastics, bromine-containing compounds can incorporated into the polymer during polymerization. One method is to include a relatively small amount of brominated monomer during the polymerization process. For example, vinyl bromide can be used in the production of polyethylene, polyvinylchloride or polypropylene. Specific highly brominated molecules can also be added that participate in the polymerization process For example, tetrabromobisphenol A can be added to polyesters or epoxy resins, where it becomes part of the polymer. Epoxys used in printed circuit boards are normally made from such flame retardant resins, indicated by the FR in the abbreviation of the products (FR-4 and FR-2). In some cases the bromine containing compound may be added after polymerization. For example, decabromodiphenyl ether can be added to the final polymers.^[35]

A number of gaseous or highly volatile brominated halomethane compounds are non-toxic and make superior fire suppressant agents by this same mechanism, and are particular effective in enclosed spaces such as submarines, airplanes, and spacecraft. However, they are expensive and their production and use has been greatly curtailed due to their effect as ozone-depleting agents. They are no longer used in routine fire extinguishers, but retain niche uses in aerospace and military automatic fire-suppression applications. They include bromochloromethane (Halon 1011, CH₂BrCl), bromochlorodifluoromethane (Halon 1211, CBrClF₂), and bromotrifluoromethane (Halon 1301, CBrF₃).

§Gasoline additive

Ethylene bromide was an additive in gasolines containing lead anti-engine knocking agents. It scavenges lead by forming volatile lead bromide, which is exhausted from the engine. This application accounted for 77% of the bromine use in 1966 in the US. This application has declined since the 1970s due to environmental regulations (see below).^[36]

§Pesticide

Methyl bromide (bromomethane)

Poisonous methyl bromide was widely used as pesticide to fumigate soil and to fumigate housing, by the tenting method. Ethylene bromide was similarly used.^[28] These volatile organobromine compounds are all now regulated as ozone depletion agents. The Montreal Protocol on Substances that Deplete the Ozone scheduled the phase out for the ozone depleting chemical by 2005, and organobromide pesticides are no longer used (in housing fumagation they have been replaced by such compounds as sulfuryl fluoride, which contain neither the chlorine or bromine organics which harm ozone). Prior to the Montreal protocol in 1991 (for example) an estimated 35,000 tonnes of the chemical were used to control nematodes, fungi, weeds and other soil-borne diseases.^[37][38]

§Medical and veterinary

Potassium bromide

Use. Bromide compounds, especially potassium bromide, were frequently used as general sedatives in the 19th and early 20th century. Bromides in the form of simple salts are still used as anticonvulsants in both veterinary and human medicine, although the latter use varies from country to country. For example, the U.S. Food and Drug Administration (FDA) does not approve bromide for the treatment of any disease, and it was removed from over-the-counter sedative products like Bromo-Seltzer, in 1975.^[39] Thus, bromide levels are not routinely measured by medical laboratories in the U.S. However, U.S. veterinary medical diagnostic testing laboratories will measure blood bromide levels on request, as an aid to treatment of epilepsy in dogs.

A bottle of PRN Pharmaceutical Company (Pensacola, FL) K•BroVet veterinary pharmaceutical potassium bromide oral solution (250 mg / mL). The product is intended to be used in dogs, primarily as an antiepileptic (to stop seizures).

Toxicity. Long-term use of potassium bromide (or any bromide salt) can lead to bromism. This state of central nervous system depression causes the moderate toxicity of bromide in multi-gram doses for humans and other mammals. The very long half-life of bromide ion in the body (~12 days) also contributes to toxicity from bromide build-up in body fluids. Bromide ingestion may also cause a skin eruption resembling acne.

§Other uses

Agarose gel stained with ethidium bromide. Ethidium bromide emits orange light when intercalating DNA and when exposed to UV light.

• The bromides of calcium, sodium, and zinc account for a sizable part of the bromine market. These salts form dense solutions in water that are used as drilling fluids sometimes called clear brine fluids.^[28][40]
• Bromine is also used in the production of brominated vegetable oil, which is used as an emulsifier in many citrus-flavored soft drinks (for example, Mountain Dew). After the introduction in the 1940s the compound was extensively used until the UK and the US limited its use in the mid 1970s and alternative emulsifiers were developed.^[41]
  Soft drinks containing brominated vegetable oil are still sold in the US (2013).^[42]

Tralomethrin

• Several dyes, agrichemicals, and pharmaceuticals are organobromine compounds. 1-Bromo-3-chloropropane, 1-bromoethylbenzene, and 1-bromoalkanes are prepared by the antimarkovnikov addition of HBr to alkenes. Ethidium bromide, EtBr, is used as a DNA stain in gel electrophoresis.
• High refractive index compounds
• Bromine, like chlorine, is used in maintenance of swimming pools, especially spas (hot tubs), where it is generated in situ from a bromide plus hydrogen peroxide. In spas, the high water temperatures render chlorinated water purification and buffering compounds unstable, and bromine compounds may improve the life of the free-halogen antimicrobial.
• Water purification compounds, disinfectants and insecticides, such as tralomethrin (C₂₂H₁₉Br₄NO₃).^[28]
• Potassium bromide is used in some photographic developers to inhibit the formation of fog (undesired reduction of silver).
• Scandium bromide is used in solid state synthesis of unusual clusters which are of interest for their structure and magnetic properties.
• Bromine vapor is used as the second step in sensitizing daguerreotype plates to be developed under mercury vapor. Bromine acts as an accelerator to the light sensitivity of the previously iodized plate.
• Bromine is also used to reduce mercury pollution from coal-fired power plants. This can be achieved either by treating activated carbon with bromine or by injecting bromine compounds onto the coal prior to combustion.
• Bromine can also be artificially substituted for the methyl substituent in the nitrogenous base thymine of DNA, creating the base analog 5-bromouracil. When this base is incorporated into DNA its different hydrogen bonding properties may cause mutation at the site of that base pair. The compound 5-bromouracil is thus an artificial mutagen.^[43]
• Aqueous bromine can be used to test for the presence of alkenes. The aqueous bromine is shaken with the unknown substance and will decolorize if alkenes are present.^[44]

§Biological role

Tyrian purple

The chemical structure of 6,6′-dibromoindigo, the main component of Tyrian Purple

Recently, bromine (as bromide) was shown to be an essential cofactor for the peroxidasin catalyzed formation of sulfilimine crosslinks in collagen IV. Since this is a post-translational modification that occurs in all animals, bromine is therefore an essential trace element for humans.^[45] Inorganic bromine and organobromine compounds also perform other biological functions, which may be essential, or at least optimal and preferred. For example, in the presence of H₂O₂ formed by the eosinophil, and either chloride or bromide ions, eosinophil peroxidase provides a potent mechanism by which eosinophils kill multicellular parasites (such as, for example, the nematode worms involved in filariasis); and also certain bacteria (such as tuberculosis bacteria). Eosinophil peroxidase is a haloperoxidase that preferentially uses bromide over chloride for this purpose, generating hypobromite (hypobromous acid).^[46] A brominated ester (2-octyl γ-bromoacetoacetate) has been shown to be produced endogenously by mammalian (including human) tissue and has been shown to prolong REM sleep in cats.^[47]

Marine organisms are the main source of organobromine compounds. Over 1600 compounds were identified by 1999. The most abundant one is methyl bromide (CH₃Br) with an estimated 56,000 tonnes produced by marine algae each year.^[48] The essential oil of the Hawaiian alga Asparagopsis taxiformis consists of 80% tribromomethane (bromoform).^[49] Most of such organobromine compounds in the sea are made via the action of a unique algal enzyme, vanadium bromoperoxidase.^[50] Though this enzyme is the most prolific creator of organic bromides by living organisms, other bromoperoxidases exist in nature that do not use vanadium.

A famous example of a bromine-containing organic compound that has been used by humans since ancient times is the fabric dye Tyrian purple.^[25][48][51] The brominated indole indigo dye is produced by a medium-sized predatory sea snail, the marine gastropod Murex brandaris. The organobromine nature of the compound was not discovered until 1909 (see Paul Friedländer).^[52]

§Safety

Elemental bromine is toxic and causes burns. As an oxidizing agent, it is incompatible with most organic and inorganic compounds. Care needs to be taken when transporting bromine; it is commonly carried in steel tanks lined with lead, supported by strong metal frames.
When certain ionic compounds containing bromine are mixed with potassium permanganate (KMnO₄) and an acidic substance, they will form a pale brown cloud of bromine gas.

6 Br⁻ + 2 MnO−
4 + 8 H⁺ → 3 Br₂ + 2 MnO₂ + 4 H₂O

This gas smells like bleach and is very irritating to the mucous membranes. Upon exposure, one should move to fresh air immediately. If symptoms of bromine poisoning arise, medical attention is needed.

Synthetic biology

From Wikipedia, the free encyclopedia

Synthetic biology is an interdisciplinary branch of biology, combining disciplines such as biotechnology, evolutionary biology, molecular biology, systems biology and biophysics, and is in many ways related to genetic engineering.

The definition of synthetic biology is heavily debated not only among natural scientists but also in the human sciences, arts and politics.^[1] One popular definition is "designing and constructing biological devices^[2] and biological systems for useful purposes." However, the functional aspects of this definition stem from molecular biology and biotechnology.^[3]

List of BioBrick parts represented with symbols

History

The term "synthetic biology" has a history spanning the twentieth century. The first use was in Stéphane Leducs’s publication of « Théorie physico-chimique de la vie et générations spontanées » (1910)^[4] and « La Biologie Synthétique » (1912).^{[5][who said this?]} In 1974, the Polish geneticist Wacław Szybalski used the term "synthetic biology",^[6] writing:

Let me now comment on the question "what next". Up to now we are working on the descriptive phase of molecular biology. ... But the real challenge will start when we enter the synthetic phase of research in our field. We will then devise new control elements and add these new modules to the existing genomes or build up wholly new genomes. This would be a field with an unlimited expansion potential and hardly any limitations to building "new better control circuits" or ..... finally other "synthetic" organisms, like a "new better mouse". ... I am not concerned that we will run out of exciting and novel ideas, ... in the synthetic biology, in general.

When in 1978 the Nobel Prize in Physiology or Medicine was awarded to Arber, Nathans and Smith for the discovery of restriction enzymes, Wacław Szybalski wrote in an editorial comment in the journal Gene:

The work on restriction nucleases not only permits us easily to construct recombinant DNA molecules and to analyze individual genes, but also has led us into the new era of synthetic biology where not only existing genes are described and analyzed but also new gene arrangements can be constructed and evaluated.^[7]

Perspectives

Engineering

Engineers view biology as a technology – the systems biotechnology or systems biological engineering.^[8] Synthetic Biology includes the broad redefinition and expansion of biotechnology, with the ultimate goals of being able to design and build engineered biological systems that process information, manipulate chemicals, fabricate materials and structures, produce energy, provide food, and maintain and enhance human health (see Biomedical Engineering) and our environment.^[9]
Studies in synthetic biology can be subdivided into broad classifications according to the approach they take to the problem at hand: standardization of biological parts, biomolecular engineering, genome engineering. Biomolecular engineering includes approaches which aim to create a toolkit of functional units that can be introduced to present new orthogonal functions in living cells. Genetic engineering includes approaches to construct synthetic chromosomes for whole or minimal organisms. Biomolecular design refers to the general idea of the de novo design and combination of biomolecular components. The task of each of these approaches is similar: To create a more synthetic entry at a higher level of complexity by manipulating a part of the preceding level.^[10]

Re-writing

Re-writers are synthetic biologists who are interested in testing the idea that since natural biological systems are so complicated, we would be better off re-building the natural systems that we care about, from the ground up, in order to provide engineered surrogates that are easier to understand and interact with.^[11] Re-writers draw inspiration from refactoring, a process sometimes used to improve computer software.

Key enabling technologies

There are several key enabling technologies that are critical to the growth of synthetic biology. The key concepts include standardization of biological parts and hierarchical abstraction to permit using those parts in increasingly complex synthetic systems.^[12] Achieving this is greatly aided by basic technologies of reading and writing of DNA (sequencing and fabrication), which are improving in price/performance exponentially (Kurzweil 2001). Measurements under a variety of conditions are needed for accurate modeling and computer-aided-design (CAD).

Standardized DNA parts

The most used^[13]:22–23 standardized DNA parts are BioBrick plasmids invented by Tom Knight in 2003.^[14] Biobricks are stored at the Registry of Standard Biological Parts in Cambridge, Massachusetts and the BioBrick standard has been used by thousands of students worldwide in the international Genetically Engineered Machine (iGEM) competition.^[13]:22–23

DNA synthesis

In 2007 it was reported that several companies were offering the synthesis of genetic sequences up to 2000 bp long, for a price of about $1 per base pair and a turnaround time of less than two weeks.^[15]
Oligonucleotides harvested from a photolithographic or inkjet manufactured DNA chip combined with DNA mismatch error-correction allows inexpensive large-scale changes of codons in genetic systems to improve gene expression or incorporate novel amino-acids (see George M. Church's and Anthony Forster's synthetic cell projects.)^[16] This favors a synthesis-from-scratch approach.

DNA sequencing

DNA sequencing is determining the order of the nucleotide bases in a molecule of DNA. Synthetic biologists make use of DNA sequencing in their work in several ways. First, large-scale genome sequencing efforts continue to provide a wealth of information on naturally occurring organisms. This information provides a rich substrate from which synthetic biologists can construct parts and devices. Second, synthetic biologists use sequencing to verify that they fabricated their engineered system as intended. Third, fast, cheap and reliable sequencing can also facilitate rapid detection and identification of synthetic systems and organisms.^[17]

Modeling

Models inform the design of engineered biological systems by allowing synthetic biologists to better predict system behavior prior to fabrication. Synthetic biology will benefit from better models of how biological molecules bind substrates and catalyze reactions, how DNA encodes the information needed to specify the cell and how multi-component integrated systems behave. Recently, multiscale models of gene regulatory networks have been developed that focus on synthetic biology applications. Simulations have been used that model all biomolecular interactions in transcription, translation, regulation, and induction of gene regulatory networks, guiding the design of synthetic systems.^[18]

Examples

Synthetic DNA

Driven by dramatic decreases in costs of making oligonucleotides ("oligos"), the sizes of DNA constructions from oligos have increased to the genomic level.^[19] For example, in 2000, researchers at Washington University reported synthesis of the 9.6 kbp (kilo base pair) Hepatitis C virus genome from chemically synthesized 60 to 80-mers.^[20] In 2002 researchers at SUNY Stony Brook succeeded in synthesizing the 7741 base poliovirus genome from its published sequence, producing the second synthetic genome. This took about two years of work.^[21] In 2003 the 5386 bp genome of the bacteriophage Phi X 174 was assembled in about two weeks.^[22] In 2006, the same team, at the J. Craig Venter Institute, had constructed and patented a synthetic genome of a novel minimal bacterium, Mycoplasma laboratorium and were working on getting it functioning in a living cell.^[23][24]

Synthetic life

One important topic in synthetic biology is synthetic life, that is, artificial life created in vitro from biochemicals and their component materials. Synthetic life experiments attempt to either probe the origins of life, study some of the properties of life, or more ambitiously to recreate life from non-alive (abiotic) substances. In May 2010, Craig Venter's group announced they had been able to assemble a complete genome of millions of base pairs, insert it into a cell, and cause that cell to start replicating.^[25] For the creation of this semi-synthetic cell, first the complete DNA sequence of the genome of a bacterium Mycoplasma mycoides was determined. A new genome was then designed based on this genome with watermarks and elements necessary for growth in yeast and genome transplantation added, as well as part of its sequence deliberately deleted. This new genome was synthesized in small fragments —over a thousand overlapping cassettes of synthetic oligonucleotides were created— which were then assembled in steps in yeast and other cells, and the complete genome was finally transplanted into a living cell from another species Mycoplasma capricolum from which all genetic material had been removed.^[26][27] The cell divided and was "entirely controlled by (the) new genome", ultimately demonstrating that DNA can be very practically described by its chemical properties.^[27] This cell has been referred to by Venter as the "first synthetic cell", and was created at a cost of over $40 million.^[27] There is some debate within the scientific community over whether this cell can be considered completely synthetic on the grounds that:^[27] the chemically synthesized genome was an almost 1:1 copy of a naturally occurring genome and, the recipient cell was a naturally occurring bacterium. The Craig Venter Institute maintains the term "synthetic bacterial cell" but they also clarify "...we do not consider this to be "creating life from scratch" but rather we are creating new life out of already existing life using synthetic DNA." ^[28] Venter plans to patent his experimental cells, stating that "they are pretty clearly human inventions".^[27] Its creators suggests that building 'synthetic life' would allow researchers to learn about life by building it, rather than by tearing it apart. They also propose to stretch the boundaries between life and machines until the two overlap to yield "truly programmable organisms."^[29] Researchers involved stated that the creation of "true synthetic biochemical life" is relatively close in reach with current technology and cheap compared to the effort needed to place a man on the Moon.^[30]

Information Storage

Scientists can encode vast amounts of digital information onto a single strand of synthetic DNA. In 2012, George M. Church encoded one of his books about synthetic biology in DNA. The 5.3 Mb of data from the book is more than 1000 times greater than the previous largest amount of information to be stored in synthesized DNA.^[31] A similar project had encoded the complete sonnets of William Shakespeare in DNA.^[32]

Synthetic genetic pathways

Traditional metabolic engineering has been bolstered by the introduction of combinations of foreign genes and optimization by directed evolution. Perhaps the best known application of synthetic biology to date is engineering E. coli and yeast for commercial production of a precursor of the antimalarial drug, Artemisinin, by the laboratory of Jay Keasling.^{[citation needed]}

Unnatural nucleotides

Many technologies have been developed for incorporating unnatural nucleotides and amino acids into nucleic acids and proteins, both in vitro and in vivo. For example, in May 2014, researchers announced that they had successfully introduced two new artificial nucleotides into bacterial DNA, and by including individual artificial nucleotides in the culture media, were able to passage the bacteria 24 times; they did not create mRNA or proteins able to use the artificial nucleotides.^[33][34][35]

Unnatural amino acids

Another common topic of investigation is expansion of the normal repertoire of 20 amino acids. Excluding stop codons, there are 61 codons, but only 20 amino acids are coded in virtually all organisms. Certain codons are engineered to code for an alternative amino acid, including nonstandard (such as O-methyl tyrosine) or exogenous (such as 4-fluorophenylalanine) amino acids. Typically, these projects make use of re-coded nonsense suppressor tRNA-Aminoacyl tRNA synthetase pairs from other organisms, though in most cases substantial engineering is still required.^[36]

Reduced amino-acid libraries

Instead of expanding the genetic code, other researchers have investigated the structure and function of proteins by reducing the normal set of 20 amino acids, that is, by generating proteins where certain groups of amino acids may be substituted with a single amino acid.^[37] For instance, several non-polar amino acids within a protein may all be replaced with a single non-polar amino acid.^[38]
One project demonstrated that an engineered version of Chorismate mutase still had catalytic activity when only 9 amino acids were used.^[39]

Designed proteins

While there are methods to engineer natural proteins (such as by Directed evolution), there are also projects to design novel protein structures that match or improve on the functionality of existing proteins. One group generated a helix bundle that was capable of binding oxygen with similar properties as hemoglobin, yet did not bind carbon monoxide.^[40] A similar protein structure was generated to support a variety of oxidoreductase activities.^[41] Another group generated a family of G-protein coupled receptors which could be activated by the inert small molecule clozapine-N-oxide but insensitive to the native ligand (acetylcholine)^[42]

Biosensors

A biosensor refers to an engineered organism (usually a bacterium) that is capable of reporting some environmental phenomenon, such the presence of heavy metals or toxins. In this respect, a very widely used system is the Lux operon of Aliivibrio fischeri. The Lux operon consists of five genes which are necessary and sufficient for bacterial bioluminescence, and can be placed under an alternate promoter to express the genes in response to an arbitrary environmental stimulus. One such sensor created in Oak Ridge National Laboratory and named “critter on a chip” used a coating of bioluminescent bacteria on a light sensitive computer chip to detect certain petroleum pollutants. When the bacteria sense the pollutant, they begin to generate light.^[43]

Materials production

By integrating synthetic biology approaches with materials sciences, it would be possible to envision cells as microscopic molecular foundries to produce materials with properties that can be genetically encoded. Recent advances towards this include reengineering curli fibers, the amyloid component of extracellular material of biofilms, as a platform for a programmable nanomaterial. These nanofibers have been genetically programmed for specific functions, including adhesion to substrates, nanoparticle templating, and protein immobilization.^[44]

Bioethics and security issues

In addition to numerous scientific and technical challenges, synthetic biology raises ethical issues and biosecurity issues. However, with the exception of regulating DNA synthesis companies,^[45] the issues are not seen as new because they were raised during the earlier recombinant DNA and genetically-modified organism (GMO) debates and there were already extensive regulations of genetic engineering and pathogen research in place in the U.S.A., Europe and the rest of the world.^[46]

The European Union funded project SYNBIOSAFE^[47] has issued several reports on how to manage the risks of synthetic biology. A 2007 paper identified key issues in the areas of safety, security, ethics and the science-society interface (the latter of which they defined as public education and as ongoing dialogue among scientists, businesses, government, and ethicists).^[48][49] Key security issues involved engaging companies that sell synthetic DNA and the Biohacking community of amateur biologists. Key ethical issues concerned the creation of new life forms. A subsequent report focused on biosecurity issues, especially the so-called dual-use challenge. For example, while the study of synthetic biology may lead to more efficient ways to produce medical treatments (e.g. against malaria, see artemisinin), it may also lead to synthesis or redesign of harmful pathogens (e.g., smallpox) by malicious actors.^[50] The bio-hacking community remains a source of special concern, as the distributed and diffuse nature of open-source biotechnology makes it difficult to track, regulate, or mitigate potential biosafety and biosecurity concerns.^[51]

COSY is another European initiative - its focus is on public perception and communication of synthetic biology.^[52][53][54] To better communicate synthetic biology and its societal ramifications to a broader public, COSY and SYNBIOSAFE published a 38-minute documentary film in October 2009.^[55]

An initiative for self-regulation has been proposed by the International Association Synthetic Biology^[56] that suggests some specific measures to be implemented by the synthetic biology industry, especially DNA synthesis companies. In 2007, a group led by scientists from leading DNA synthesis companies published a "practical plan for developing an effective oversight framework for the DNA-synthesis industry."^[45]

In January 2009, the Alfred P. Sloan Foundation funded the Woodrow Wilson Center, the Hastings Center, and the J. Craig Venter Institute to examine the public perception, ethics, and policy implications of synthetic biology.^[57]

On July 9–10, 2009, the National Academies' Committee of Science, Technology & Law convened a symposium on "Opportunities and Challenges in the Emerging Field of Synthetic Biology".^[58]

After the publication of the first synthetic genome by Craig Venter's group and the accompanying media coverage about "life" being created, President Obama requested the Presidential Commission for the Study of Bioethical Issues to study synthetic biology.^[59] The commission convened a series of meetings, then issued a report in December 2010 titled "New Directions: The Ethics of Synthetic Biology and Emerging Technologies." The report clarified that the Venter group had not created life, and noted that synthetic biology is an emerging field, which creates potential risks and rewards. The commission did not recommend any changes to policy or oversight and called for continued funding of the research and new funding for monitoring, study of emerging ethical issues, and public education.^[46]

Opposition to synthetic biology

On March 13, 2012, over 100 environmental and civil society groups, including Friends of the Earth, the International Center for Technology Assessment and the ETC Group issued the manifesto The Principles for the Oversight of Synthetic Biology which call for a worldwide moratorium on the release and commercial use of synthetic organisms until more robust regulations and rigorous biosafety measures are established. The groups specifically call for an outright ban on the use of synthetic biology on the human genome or human microbiome.^[60][61] Richard Lewontin wrote that some of the safety tenets for oversight discussed in The Principles for the Oversight of Synthetic Biology are reasonable, but that the main problem with the recommendations in the manifesto is that "the public at large lacks the ability to enforce any meaningful realization of those recommendations."^[62]