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Asexual reproduction

Asexual reproduction is a type of reproduction that does not involve the fusion of gametes or change in the number of chromosomes. The offspring that arise by asexual reproduction from either unicellular or multicellular organisms inherit the full set of genes of their single parent and thus the newly created individual is genetically and physically similar to the parent or an exact clone of the parent. Asexual reproduction is the primary form of reproduction for single-celled organisms such as archaea and bacteria. Many eukaryotic organisms including plants, animals, and fungi can also reproduce asexually. In vertebrates, the most common form of asexual reproduction is parthenogenesis, which is typically used as an alternative to sexual reproduction in times when reproductive opportunities are limited. Komodo dragons and some monitor lizards can reproduce asexually.

While all prokaryotes reproduce without the formation and fusion of gametes, mechanisms for lateral gene transfer such as conjugation, transformation and transduction can be likened to sexual reproduction in the sense of genetic recombination in meiosis.

Fission
Prokaryotes (Archaea and Bacteria) reproduce asexually through binary fission, in which the parent organism divides in two to produce two genetically identical daughter organisms. Eukaryotes (such as protists and unicellular fungi) may reproduce in a functionally similar manner by mitosis; most of these are also capable of sexual reproduction.

Multiple fission at the cellular level occurs in many protists, e.g. sporozoans and algae. The nucleus of the parent cell divides several times by mitosis, producing several nuclei. The cytoplasm then separates, creating multiple daughter cells.

In apicomplexans, multiple fission, or schizogony appears either as merogony, sporogony or gametogony. Merogony results in merozoites, which are multiple daughter cells, that originate within the same cell membrane, sporogony results in sporozoites, and gametogony results in microgametes.

Budding

Some cells divide by budding (for example baker's yeast), resulting in a "mother" and a "daughter" cell that is initially smaller than the parent. Budding is also known on a multicellular level; an animal example is the hydra, which reproduces by budding. The buds grow into fully matured individuals which eventually break away from the parent organism.

Internal budding is a process of asexual reproduction, favoured by parasites such as Toxoplasma gondii. It involves an unusual process in which two (endodyogeny) or more (endopolygeny) daughter cells are produced inside a mother cell, which is then consumed by the offspring prior to their separation.

Also, budding (external or internal) occurs in some worms like Taenia or Echinococcus; these worms produce cysts and then produce (invaginated or evaginated) protoscolex with budding.

Vegetative propagation

Vegetative propagation is a type of asexual reproduction found in plants where new individuals are formed without the production of seeds or spores and thus without syngamy or meiosis. Examples of vegetative reproduction include the formation of miniaturized plants called plantlets on specialized leaves, for example in kalanchoe (Bryophyllum daigremontianum) and many produce new plants from rhizomes or stolon (for example in strawberry). Some plants reproduce by forming bulbs or tubers, for example tulip bulbs and Dahlia tubers. In these examples, all the individuals are clones, and the clonal population may cover a large area.

Spore formation
Many multicellular organisms produce spores during their biological life cycle in a process called sporogenesis. Exceptions are animals and some protists, which undergo meiosis immediately followed by fertilization. Plants and many algae on the other hand undergo sporic meiosis where meiosis leads to the formation of haploid spores rather than gametes. These spores grow into multicellular individuals called gametophytes, without a fertilization event. These haploid individuals produce gametes through mitosis. Meiosis and gamete formation therefore occur in separate multicellular generations or "phases" of the life cycle, referred to as alternation of generations. Since sexual reproduction is often more narrowly defined as the fusion of gametes (fertilization), spore formation in plant sporophytes and algae might be considered a form of asexual reproduction (agamogenesis) despite being the result of meiosis and undergoing a reduction in ploidy. However, both events (spore formation and fertilization) are necessary to complete sexual reproduction in the plant life cycle.

Fungi and some algae can also utilize true asexual spore formation, which involves mitosis giving rise to reproductive cells called mitospores that develop into a new organism after dispersal. This method of reproduction is found for example in conidial fungi and the red algae Polysiphonia, and involves sporogenesis without meiosis. Thus the chromosome number of the spore cell is the same as that of the parent producing the spores. However, mitotic sporogenesis is an exception and most spores, such as those of plants and many algae, are produced by meiosis.

Fragmentation

Fragmentation is a form of asexual reproduction where a new organism grows from a fragment of the parent. Each fragment develops into a mature, fully grown individual. Fragmentation is seen in many organisms. Animals that reproduce asexually include planarians, many annelid worms including polychaetes and some oligochaetes, turbellarians and sea stars. Many fungi and plants reproduce asexually. Some plants have specialized structures for reproduction via fragmentation, such as gemmae in mosses and liverworts. Most lichens, which are a symbiotic union of a fungus and photosynthetic algae or cyanobacteria, reproduce through fragmentation to ensure that new individuals contain both symbionts. These fragments can take the form of soredia, dust-like particles consisting of fungal hyphae wrapped around photobiont cells.

Clonal Fragmentation in multicellular or colonial organisms is a form of asexual reproduction or cloning where an organism is split into fragments. Each of these fragments develop into mature, fully grown individuals that are clones of the original organism. In echinoderms, this method of reproduction is usually known as fissiparity. Due to many environmental and epigenetic differences, clones originating from the same ancestor might actually be genetically and epigenetically different.

Agamogenesis
Agamogenesis is any form of reproduction that does not involve a male gamete. Examples are parthenogenesis and apomixis.

Parthenogenesis
Parthenogenesis is a form of agamogenesis in which an unfertilized egg develops into a new individual. It has been documented in over 2,000 species. Parthenogenesis occurs in the wild in many invertebrates (e.g. water fleas, rotifers, aphids, stick insects, some ants, bees and parasitic wasps) and vertebrates (mostly reptiles, amphibians, and fish). It has also been documented in domestic birds and in genetically altered lab mice. Plants can engage in parthenogenesis as well through a process called apomixis. However this process is considered by many to not be an independent reproduction method, but instead a breakdown of the mechanisms behind sexual reproduction. Parthenogenetic organisms can be split into two main categories: facultative and obligate.

Facultative parthenogenesis
In facultative parthenogenesis, females can reproduce both sexually and asexually. Because of the many advantages of sexual reproduction, most facultative parthenotes only reproduce asexually when forced to. This typically occurs in instances when finding a mate becomes difficult. For example, female zebra sharks will reproduce asexually if they are unable to find a mate in their ocean habitats.

Parthenogenesis was previously believed to rarely occur in vertebrates, and only be possible in very small animals. However, it has been discovered in many more species in recent years. Today, the largest species that has been documented reproducing parthenogenically is the Komodo dragon at 10 feet long and over 300 pounds. Heterogony is a form of facultative parthenogenesis where females alternate between sexual and asexual reproduction at regular intervals (see Alternation between sexual and asexual reproduction). Aphids are one group of organism that engages in this type of reproduction. They use asexual reproduction to reproduce quickly and create winged offspring that can colonize new plants and reproduce sexually in the fall to lay eggs for the next season. However, some aphid species are obligate parthenotes.

Obligate parthenogenesis
In obligate parthenogenesis, females only reproduce asexually. One example of this is the desert grassland whiptail lizard, a hybrid of two other species. Typically hybrids are infertile but through parthenogenesis this species has been able to develop stable populations.

Gynogenesis is a form of obligate parthenogenesis where a sperm cell is used to initiate reproduction. However, the sperm's genes never get incorporated into the egg cell. The best known example of this is the Amazon molly. Because they are obligate parthenotes, there are no males in their species so they depend on males from a closely related species (the Sailfin molly) for sperm.

Apomixis and nucellar embryony
Apomixis in plants is the formation of a new sporophyte without fertilization. It is important in ferns and in flowering plants, but is very rare in other seed plants. In flowering plants, the term "apomixis" is now most often used for agamospermy, the formation of seeds without fertilization, but was once used to include vegetative reproduction. An example of an apomictic plant would be the triploid European dandelion. Apomixis mainly occurs in two forms: In gametophytic apomixis, the embryo arises from an unfertilized egg within a diploid embryo sac that was formed without completing meiosis. In nucellar embryony, the embryo is formed from the diploid nucellus tissue surrounding the embryo sac. Nucellar embryony occurs in some citrus seeds. Male apomixis can occur in rare cases, such as in the Saharan Cypress Cupressus dupreziana, where the genetic material of the embryo is derived entirely from pollen.

Alternation between sexual and asexual reproduction
Some species can alternate between sexual and asexual strategies, an ability known as heterogamy, depending on many conditions. Alternation is observed in several rotifer species (cyclical parthenogenesis e.g. in Brachionus species) and a few types of insects.

One example of this is aphids which can engage in heterogony. In this system, females are born pregnant and produce only female offspring. This cycle allows them to reproduce very quickly. However, most species reproduce sexually once a year. This switch is triggered by environmental changes in the fall and causes females to develop eggs instead of embryos. This dynamic reproductive cycle allows them to produce specialized offspring with polyphenism, a type of polymorphism where different phenotypes have evolved to carry out specific tasks.

The cape bee Apis mellifera subsp. capensis can reproduce asexually through a process called thelytoky. The freshwater crustacean Daphnia reproduces by parthenogenesis in the spring to rapidly populate ponds, then switches to sexual reproduction as the intensity of competition and predation increases. Monogonont rotifers of the genus Brachionus reproduce via cyclical parthenogenesis: at low population densities females produce asexually and at higher densities a chemical cue accumulates and induces the transition to sexual reproduction. Many protists and fungi alternate between sexual and asexual reproduction. A few species of amphibians, reptiles, and birds have a similar ability.

The slime mold Dictyostelium undergoes binary fission (mitosis) as single-celled amoebae under favorable conditions. However, when conditions turn unfavorable, the cells aggregate and follow one of two different developmental pathways, depending on conditions. In the social pathway, they form a multi-cellular slug which then forms a fruiting body with asexually generated spores. In the sexual pathway, two cells fuse to form a giant cell that develops into a large cyst. When this macrocyst germinates, it releases hundreds of amoebic cells that are the product of meiotic recombination between the original two cells.

The hyphae of the common mold (Rhizopus) are capable of producing both mitotic as well as meiotic spores. Many algae similarly switch between sexual and asexual reproduction. A number of plants use both sexual and asexual means to produce new plants, some species alter their primary modes of reproduction from sexual to asexual under varying environmental conditions.

Inheritance in asexual species
In the rotifer Brachionus calyciflorus asexual reproduction (obligate parthenogenesis) can be inherited by a recessive allele, which leads to loss of sexual reproduction in homozygous offspring.

Inheritance of asexual reproduction by a single recessive locus has also been found in the parasitoid wasp Lysiphlebus fabarum.

Examples in animals
Asexual reproduction is found in nearly half of the animal phyla. Parthenogenesis occurs in the hammerhead shark and the blacktip shark. In both cases, the sharks had reached sexual maturity in captivity in the absence of males, and in both cases the offspring were shown to be genetically identical to the mothers. The New Mexico whiptail is another example.

Some reptiles use the ZW sex-determination system, which produces either males (with ZZ sex chromosomes) or females (with ZW or WW sex chromosomes). Until 2010, it was thought that the ZW chromosome system used by reptiles was incapable of producing viable WW offspring, but a (ZW) female boa constrictor was discovered to have produced viable female offspring with WW chromosomes. The female boa could have chosen any number of male partners (and had successfully in the past) but on this occasion she reproduced asexually, creating 22 female babies with WW sex-chromosomes.

Polyembryony is a widespread form of asexual reproduction in animals, whereby the fertilized egg or a later stage of embryonic development splits to form genetically identical clones. Within animals, this phenomenon has been best studied in the parasitic Hymenoptera. In the nine-banded armadillos, this process is obligatory and usually gives rise to genetically identical quadruplets. In other mammals, monozygotic twinning has no apparent genetic basis, though its occurrence is common. There are at least 10 million identical human twins and triplets in the world today.

Bdelloid rotifers reproduce exclusively asexually, and all individuals in the class Bdelloidea are females. Asexuality evolved in these animals millions of years ago and has persisted since. There is evidence to suggest that asexual reproduction has allowed the animals to evolve new proteins through the Meselson effect that have allowed them to survive better in periods of dehydration. Bdelloid rotifers are extraordinarily resistant to damage from ionizing radiation due to the same DNA-preserving adaptations used to survive dormancy. These adaptations include an extremely efficient mechanism for repairing DNA double-strand breaks. This repair mechanism was studied in two Bdelloidea species, Adineta vaga, and Philodina roseola. and appears to involve mitotic recombination between homologous DNA regions within each species.

Molecular evidence strongly suggests that several species of the stick insect genus Timema have used only asexual (parthenogenetic) reproduction for millions of years, the longest period known for any insect. Similar findings suggest that the mite species Oppiella nova may have reproduced entirely asexually for millions of years.

In the grass thrips genus Aptinothrips there have been several transitions to asexuality, likely due to different causes.

Adaptive significance of asexual reproduction
A complete lack of sexual reproduction is relatively rare among multicellular organisms, particularly animals. It is not entirely understood why the ability to reproduce sexually is so common among them. Current hypotheses suggest that asexual reproduction may have short term benefits when rapid population growth is important or in stable environments, while sexual reproduction offers a net advantage by allowing more rapid generation of genetic diversity, allowing adaptation to changing environments. Developmental constraints may underlie why few animals have relinquished sexual reproduction completely in their life-cycles. Almost all asexual modes of reproduction maintain meiosis either in a modified form or as an alternative pathway. Facultatively apomictic plants increase frequencies of sexuality relative to apomixis after abiotic stress. Another constraint on switching from sexual to asexual reproduction would be the concomitant loss of meiosis and the protective recombinational repair of DNA damage afforded as one function of meiosis.

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Talk:Acantharea

Untitled
''Is this a family, genus, or what? article just says "group".''

That was deliberate. Right now relationships among the major groups of protists are very unclear, so many workers in the field have abandoned taxonomic ranks for the time being, and the remainder don't pay very much attention to them. This is simply because they are too likely to change back and forth to be of any use. The Acantharea themselves are variously ranked as anything from a subclass (or even order) up to a phylum, depending on whether one tries to retain the Radiolaria, Actinopoda and Sarcodina as taxa, replace them with other groups, or simply abandon them and promote the subdivisions. I figured it would be best not to worry about this and leave them unranked until some day when the taxonomy hopefully stabilizes.

I am not a fan of abandoning taxonomic levels but in this case it is almost certainly sensibleJeremy Young (talk) 15:19, 28 January 2009 (UTC)

Structure
I would like to recommend that the subject of "Müllerian law" be moved to a separate article on that subject. This would allow reference to that article and removal of the explanation of that law within this article, thus cleaning the structure of this article. I do not have the background or expertise to write such an article. It appears that other forms of life have "spines" following this pattern. I assume this because the easiest reference I can find to "Müllerian law" is "Müllerian law of Icosacantha" within the reports from the H.M.S. Challenger Voyage of Exploration (1873-1877). Within these reports, there are many references to this law in conjunction with different species. If I am incorrect, and the species names referenced in this very old set of documents all relate to the subject of this article, in short, if this law only applies to Acantharea, then please disregard this recommendation. — Preceding unsigned comment added by Sdfosterc (talk • contribs) 00:02, 15 October 2013 (UTC)

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

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Aelbert Cuyp

Aelbert Jacobszoon Cuyp or Cuijp (20 October 1620 – 15 November 1691) was one of the leading Dutch Golden Age painters, producing mainly landscapes. The most famous of a family of painters, the pupil of his father, Jacob Gerritszoon Cuyp (1594–1651/52), he is especially known for his large views of Dutch riverside scenes in a golden early morning or late afternoon light. He was born and died in Dordrecht.

Biography
Known as the Dutch equivalent of Claude Lorrain, he inherited a considerable fortune. His family were all artists, with his uncle Benjamin and grandfather Gerrit being stained glass cartoon designers. Jacob Gerritszoon Cuyp, his father, was a portraitist. Cuyp's father was his first teacher and they collaborated on many paintings throughout his lifetime. Little is known about Aelbert Cuyp's life. Even Arnold Houbraken, a noted historian of Dutch Golden Age paintings and the sole authority on Cuyp for the hundred years following his death, paints a very thin biographical picture.

His period of activity as a painter is traditionally limited to the two decades between 1639 and 1660, fitting within the generally accepted limits of the Dutch Golden Age's most significant period, 1640–1665. He is known to have been married to Cornelia Bosman in 1658, a date coinciding so directly with the end of his productivity as a painter that it has been accepted that his marriage played a role in the end of his artistic career.

The year after his marriage, Cuyp became the deacon of the reformed church. Houbraken recalled that Cuyp was a devout Calvinist and the fact that when he died, there were no paintings of other artists found in his home.

Style
The development of Cuyp, who was trained as a landscape painter, may be roughly sketched in three phases based on the painters who most influenced him during that time and the subsequent artistic characteristics that are apparent in his paintings. Generally, Cuyp learned tone from the exceptionally prolific Jan van Goyen, light from Jan Both and form from his father, Jacob Gerritsz Cuyp.

Cuyp's "van Goyen phase" can be placed approximately in the early 1640s. Cuyp probably first encountered a painting by van Goyen in 1640 when van Goyen was, as Stephen Reiss points, out "at the height of [his] powers". This is noticeable in the comparison between two of Cuyp's landscape paintings inscribed 1639 where no properly formed style is apparent and the landscape backgrounds he painted two years later for two of his father's group portraits that are distinctly van Goyenesque. Cuyp took from van Goyen the straw yellow and light brown tones that are so apparent in his Dunes (1629) and the broken brush technique also very noticeable in that same work. This technique, a precursor to impressionism, is noted for the short brush strokes where the colors are not necessarily blended smoothly. In Cuyp's River Scene, Two Men Conversing (1641) both of these van Goyen-influenced stylistic elements are noticeable.

The next phase in the development of Cuyp's increasingly amalgamated style is due to the influence of Jan Both. In the mid-1640s Both, a native and resident of Utrecht, had just returned to his hometown from a trip to Rome. It is around this same time that Cuyp's style changed fundamentally. In Rome, Both had developed a new style of composition due, at least in part, to his interaction with Claude Lorrain. This new style was focused on changing the direction of light in the painting. Instead of the light being placed at right angles in relation to the line of vision, Both started moving it to a diagonal position from the back of the picture.

In this new form of lighting, the artist (and viewer of the painting) faced the sun more or less contre-jour. Both, and subsequently Cuyp, used the advantages of this new lighting style to alter the sense of depth and luminosity possible in a painting. To make notice of these new capabilities, much use was made of elongated shadows. Cuyp was one of the first Dutch painters to appreciate this new leap forward in style and while his own Both-inspired phase was quite short (limited to the mid-1640s) he did, more than any other contemporary Dutch artist, maximize the full chromatic scale for sunsets and sunrises. Cuyp's third stylistic phase (which occurred throughout his career) is based on the influence of his father. While it is assumed that the younger Cuyp did work with his father initially to develop rudimentary talents, Aelbert became more focused on landscape paintings while Jacob was a portrait painter by profession. As has been mentioned and as will be explained in depth below, there are pieces where Aelbert provided the landscape background for his father's portraits. What is meant by stating that Aelbert learned from his father is that his eventual transition from a specifically landscape painter to the involvement of foreground figures is attributed to his interaction with his father Jacob. The evidence for Aelbert's evolution to foreground figure painter is in the production of some paintings from 1645 to 1650 featuring foreground animals that do not fit with Jacob's style. Adding to the confusion regarding Aelbert's stylistic development and the problem of attribution is of course the fact that Jacob's style was not stagnant either. Their converging styles make it difficult to exactly understand the influences each had on the other, although it is clear enough to say that Aelbert started representing large scale forms (something he had not done previously) and placing animals as the focus of his paintings (something that was specific to him).

Paintings
Sunlight in his paintings rakes across the panel, accentuating small bits of detail in the golden light. In large, atmospheric panoramas of the countryside, the highlights on a blade of meadow grass, the mane of a tranquil horse, the horn of a dairy cow reclining by a stream, or the tip of a peasant's hat are all caught in a bath of yellow ocher light. The richly varnished medium refracts the rays of light like a jewel as it dissolves into numerous glazed layers. Cuyp's landscapes were based on reality and on his own invention of what an enchanting landscape should be.Cuyp's drawings reveal him to be a draftsman of superior quality. Light-drenched washes of golden brown ink depict a distant view of the city of Dordrecht or Utrecht. A Cuyp drawing may look like he intended it to be a finished work of art, but it was most likely taken back to the studio and used as a reference for his paintings. Often the same section of a sketch can be found in several different pictures.

Cuyp signed many of his works but rarely dated them, so that a chronology of his career has not been satisfactorily reassembled. A phenomenal number of paintings are ascribed to him, some of which are likely to be by other masters of the golden landscape, such as Abraham Calraet (1642–1722), whose initials A.C. may be mistaken for Cuyp's.

However, not everyone appreciates his work and River Landscape (1660), despite being widely regarded as amongst his best work, has been described as having "chocolate box blandness".

At the Madrid's Thyssen-Bornemisza Museum most likely, the sole Cuyp's painting in Spanish public collections can be seen, a Landscape with a sunset ca. 1655 with animals.

Misattribution of paintings

In addition to the scarcely documented and confirmed biography of Cuyp's life, and even more so than his amalgamated style from his three main influences, there are yet other factors that have led to the misattribution and confusion over Aelbert Cuyp's works for hundreds of years. His highly influenced style which incorporated Italianate lighting from Jan Both, broken brush technique and atonality from Jan van Goyen, and his ever-developing style from his father Jacob Gerritsz Cuyp was studied acutely by his most prominent follower, Abraham van Calraet. Calraet mimicked Cuyp's style, incorporating the same aspects, and produced similar landscapes to that of the latter. This made it quite difficult to tell whose paintings were whose. Adding to the confusion is the similar initials between the two and the inconsistent signing of paintings which were produced by Cuyp's studio.

Although Aelbert Cuyp signed many of his paintings with a script "A. Cuyp" insignia, many paintings were left unsigned (not to mention undated) after being painted, and so a similar signature was added later on, presumably by collectors who inherited or discovered the works. Furthermore, many possible Cuyp paintings were not signed but rather initialed "A. C." referring to his name. However, Abraham van Calraet could also have used the same initials to denote a painting. Although this is unlikely (as Calraet would likely have signed his paintings "A. v.C."), this brings up the question of how paintings were signed to show ownership. Most original Cuyp paintings were signed by him, and in the script manner in which his name was inscribed. This would denote that the painting was done almost entirely by him. Conversely, paintings which came out of his workshop that were not necessarily physically worked on by Cuyp but merely overseen by him technically, were marked with A.C. to show that it was his instruction which saw the paintings' completion. Cuyp's pupils and assistants often worked on paintings in his studio, and so most of the work of a painting could be done without Cuyp ever touching the canvas, but merely approving its finality. Hence, the initialed inscription rather than a signature.

Common among the mislabeled works are all of the reasons identified for misattributing Cuyp's works: the lack of biography and chronology of his works made it difficult to discern when paintings were created (making it difficult to pinpoint an artist); contentious signatures added to historians' confusion as to who actually painted the works; and the collaborations and influences by different painters makes it hard to justify that a painting is genuinely that of Aelbert Cuyp; and finally, accurate identification is made extremely difficult by the fact that this same style was copied (rather accurately) by his predecessor. As it turns out, even the historians and expert researchers have been fooled and forced to reassess their conclusions over "Cuyp's" paintings over the years.

Later life
After he married Cornelia Boschman in 1658, the number of works produced by him declined almost to nothing. This may have been because his wife was a very religious woman and a not very big patron of the arts. It could also be that he became more active in the church under his wife's guidance. He was also active as deacon and elder of the Reformed Church.

Legacy
Though long lacking a modern biography, and with the chronology of his works rather unclear, his style emerged from various influences and makes his works distinctive, although his collaborations with his father and works by his imitators often make attributions uncertain. His follower Abraham van Calraet represents a particular problem, and the signatures on paintings are not to be relied on. The Rijksmuseum has reattributed many works to other painters; Abraham van Calraet does not even appear in a Museum catalogue until 1926, and even then he was not given his own entry.

title: Aelbert Cuyp


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Alkene

In organic chemistry, an alkene, or olefin, is a hydrocarbon containing a carbon–carbon double bond. The double bond may be internal or in the terminal position. Terminal alkenes are also known as α-olefins.

The International Union of Pure and Applied Chemistry (IUPAC) recommends using the name "alkene" only for acyclic hydrocarbons with just one double bond; alkadiene, alkatriene, etc., or polyene for acyclic hydrocarbons with two or more double bonds; cycloalkene, cycloalkadiene, etc. for cyclic ones; and "olefin" for the general class – cyclic or acyclic, with one or more double bonds.

Acyclic alkenes, with only one double bond and no other functional groups (also known as mono-enes) form a homologous series of hydrocarbons with the general formula C_{n}H_{2n} with n being a >1 natural number (which is two hydrogens less than the corresponding alkane). When n is four or more, isomers are possible, distinguished by the position and conformation of the double bond.

Alkenes are generally colorless non-polar compounds, somewhat similar to alkanes but more reactive. The first few members of the series are gases or liquids at room temperature. The simplest alkene, ethylene (C2H4) (or "ethene" in the IUPAC nomenclature) is the organic compound produced on the largest scale industrially.

Aromatic compounds are often drawn as cyclic alkenes, however their structure and properties are sufficiently distinct that they are not classified as alkenes or olefins. Hydrocarbons with two overlapping double bonds (C\dC\dC) are called allenes—the simplest such compound is itself called allene—and those with three or more overlapping bonds (C\dC\dC\dC, C\dC\dC\dC\dC, etc.) are called cumulenes.

Structural isomerism
Alkenes having four or more carbon atoms can form diverse structural isomers. Most alkenes are also isomers of cycloalkanes. Acyclic alkene structural isomers with only one double bond follow:

 * C2H4: ethylene only
 * C3H6: propylene only
 * C4H8: 3 isomers: 1-butene, 2-butene, and isobutylene
 * C5H10: 5 isomers: 1-pentene, 2-pentene, 2-methyl-1-butene, 3-methyl-1-butene, 2-methyl-2-butene
 * C6H12: 13 isomers: 1-hexene, 2-hexene, 3-hexene, 2-methyl-1-pentene, 3-methyl-1-pentene, 4-methyl-1-pentene, 2-methyl-2-pentene, 3-methyl-2-pentene, 4-methyl-2-pentene, 2,3-dimethyl-1-butene, 3,3-dimethyl-1-butene, 2,3-dimethyl-2-butene, 2-ethyl-1-butene

Many of these molecules exhibit cis–trans isomerism. There may also be chiral carbon atoms particularly within the larger molecules (from C5). The number of potential isomers increases rapidly with additional carbon atoms.

Bonding
A carbon–carbon double bond consists of a sigma bond and a pi bond. This double bond is stronger than a single covalent bond (611 kJ/mol for C=C vs. 347 kJ/mol for C–C), but not twice as strong. Double bonds are shorter than single bonds with an average bond length of 1.33 Å (133 pm) vs 1.53 Å for a typical C-C single bond.

Each carbon atom of the double bond uses its three sp2 hybrid orbitals to form sigma bonds to three atoms (the other carbon atom and two hydrogen atoms). The unhybridized 2p atomic orbitals, which lie perpendicular to the plane created by the axes of the three sp2 hybrid orbitals, combine to form the pi bond. This bond lies outside the main C–C axis, with half of the bond on one side of the molecule and a half on the other. With a strength of 65 kcal/mol, the pi bond is significantly weaker than the sigma bond.

Rotation about the carbon–carbon double bond is restricted because it incurs an energetic cost to break the alignment of the p orbitals on the two carbon atoms. Consequently cis or trans isomers interconvert so slowly that they can be freely handled at ambient conditions without isomerization. More complex alkenes may be named with the E–Z notation for molecules with three or four different substituents (side groups). For example, of the isomers of butene, the two methyl groups of (Z)-but-2-ene (a.k.a. cis-2-butene) appear on the same side of the double bond, and in (E)-but-2-ene (a.k.a. trans-2-butene) the methyl groups appear on opposite sides. These two isomers of butene have distinct properties.

Shape
As predicted by the VSEPR model of electron pair repulsion, the molecular geometry of alkenes includes bond angles about each carbon atom in a double bond of about 120°. The angle may vary because of steric strain introduced by nonbonded interactions between functional groups attached to the carbon atoms of the double bond. For example, the C–C–C bond angle in propylene is 123.9°.

For bridged alkenes, Bredt's rule states that a double bond cannot occur at the bridgehead of a bridged ring system unless the rings are large enough. Following Fawcett and defining S as the total number of non-bridgehead atoms in the rings, bicyclic systems require S ≥ 7 for stability and tricyclic systems require S ≥ 11.

Isomerism
In organic chemistry,the prefixes cis- and trans- are used to describe the positions of functional groups attached to carbon atoms joined by a double bond. In Latin, cis and trans mean "on this side of" and "on the other side of" respectively. Therefore, if the functional groups are both on the same side of the carbon chain, the bond is said to have cis- configuration, otherwise (i.e. the functional groups are on the opposite side of the carbon chain), the bond is said to have trans- configuration.

For there to be cis- and trans- configurations, there must be a carbon chain, or at least one functional group attached to each carbon is the same for both. E- and Z- configuration can be used instead in a more general case where all four functional groups attached to carbon atoms in a double bond are different. E- and Z- are abbreviations of German words zusammen (together) and entgegen (opposite). In E- and Z-isomerism, each functional group is assigned a priority based on the Cahn–Ingold–Prelog priority rules. If the two groups with higher priority are on the same side of the double bond, the bond is assigned Z- configuration, otherwise (i.e. the two groups with higher priority are on the opposite side of the double bond), the bond is assigned E- configuration. Cis- and trans- configurations do not have a fixed relationship with E- and Z-configurations.

Physical properties
Many of the physical properties of alkenes and alkanes are similar: they are colorless, nonpolar, and combustible. The physical state depends on molecular mass: like the corresponding saturated hydrocarbons, the simplest alkenes (ethylene, propylene, and butene) are gases at room temperature. Linear alkenes of approximately five to sixteen carbon atoms are liquids, and higher alkenes are waxy solids. The melting point of the solids also increases with increase in molecular mass.

Alkenes generally have stronger smells than their corresponding alkanes. Ethylene has a sweet and musty odor. Strained alkenes, in particular, like norbornene and trans-cyclooctene are known to have strong, unpleasant odors, a fact consistent with the stronger π complexes they form with metal ions including copper.

Boiling and melting points
Below is a list of the boiling and melting points of various alkenes with the corresponding alkane and alkyne analogues.

Infrared spectroscopy
The stretching of C=C bond will give an IR absorption peak at 1670–1600 cm−1, while the bending of C=C bond absorbs between 1000 and 650 cm−1 wavelength.

NMR spectroscopy
In 1H NMR spectroscopy, the hydrogen bonded to the carbon adjacent to double bonds will give a δH of 4.5–6.5 ppm. The double bond will also deshield the hydrogen attached to the carbons adjacent to sp2 carbons, and this generates δH=1.6–2. ppm peaks. Cis/trans isomers are distinguishable due to different J-coupling effect. Cis vicinal hydrogens will have coupling constants in the range of 6–14 Hz, whereas the trans will have coupling constants of 11–18 Hz.

In their 13C NMR spectra of alkenes, double bonds also deshield the carbons, making them have low field shift. C=C double bonds usually have chemical shift of about 100–170 ppm.

Combustion
Like most other hydrocarbons, alkenes combust to give carbon dioxide and water.

The combustion of alkenes release less energy than burning same molarity of saturated ones with same number of carbons. This trend can be clearly seen in the list of standard enthalpy of combustion of hydrocarbons.

Reactions
Alkenes are relatively stable compounds, but are more reactive than alkanes. Most reactions of alkenes involve additions to this pi bond, forming new single bonds. Alkenes serve as a feedstock for the petrochemical industry because they can participate in a wide variety of reactions, prominently polymerization and alkylation. Except for ethylene, alkenes have two sites of reactivity: the carbon–carbon pi-bond and the presence of allylic CH centers. The former dominates but the allylic sites are important too.

Addition to the unsaturated bonds
Hydrogenation involves the addition of H2 resulting in an alkane. The equation of hydrogenation of ethylene to form ethane is:
 * H2C=CH2 + H2→H3C−CH3

Hydrogenation reactions usually require catalysts to increase their reaction rate. The total number of hydrogens that can be added to an unsaturated hydrocarbon depends on its degree of unsaturation.

Similar to hydrogen, halogens added to double bonds.
 * H2C=CH2 + Br2→H2CBr−CH2Br

Halonium ions are intermediates. These reactions do not require catalysts.

Bromine test is used to test the saturation of hydrocarbons. The bromine test can also be used as an indication of the degree of unsaturation for unsaturated hydrocarbons. Bromine number is defined as gram of bromine able to react with 100g of product. Similar as hydrogenation, the halogenation of bromine is also depend on the number of π bond. A higher bromine number indicates higher degree of unsaturation.

The π bonds of alkenes hydrocarbons are also susceptible to hydration. The reaction usually involves strong acid as catalyst. The first step in hydration often involves formation of a carbocation. The net result of the reaction will be an alcohol. The reaction equation for hydration of ethylene is:
 * H2C=CH2 + H2O→

Hydrohalogenation involves addition of H−X to unsaturated hydrocarbons. This reaction results in new C−H and C−X σ bonds. The formation of the intermediate carbocation is selective and follows Markovnikov's rule. The hydrohalogenation of alkene will result in haloalkane. The reaction equation of HBr addition to ethylene is:
 * H2C=CH2 + HBr →

Cycloaddition
Alkenes add to dienes to give cyclohexenes. This conversion is an example of a Diels-Alder reaction. Such reaction proceed with retention of stereochemistry. The rates are sensitive to electron-withdrawing or electron-donating substituents. When irradiated by UV-light, alkenes dimerize to give cyclobutanes. Another example is the Schenck ene reaction, in which singlet oxygen reacts with an allylic structure to give a transposed allyl peroxide:

Oxidation
Alkenes react with percarboxylic acids and even hydrogen peroxide to yield epoxides:
 * RCH\dCH2 + RCO3H  ->  RCHOCH2 + RCO2H

For ethylene, the epoxidation is conducted on a very large scale industrially using oxygen in the presence of silver-based catalysts:
 * C2H4 + 1/2 O2 -> C2H4O

Alkenes react with ozone, leading to the scission of the double bond. The process is called ozonolysis. Often the reaction procedure includes a mild reductant, such as dimethylsulfide (SMe2):
 * RCH\dCHR' + O3  +  SMe2  -> RCHO  +  R'CHO  +  O\dSMe2
 * R2C\dCHR' + O3  ->  R2CHO  +  R'CHO  +  O\dSMe2

When treated with a hot concentrated, acidified solution of KMnO4, alkenes are cleaved to form ketones and/or carboxylic acids. The stoichiometry of the reaction is sensitive to conditions. This reaction and the ozonolysis can be used to determine the position of a double bond in an unknown alkene.

The oxidation can be stopped at the vicinal diol rather than full cleavage of the alkene by using osmium tetroxide or other oxidants:

This reaction is called dihydroxylation.

In the presence of an appropriate photosensitiser, such as methylene blue and light, alkenes can undergo reaction with reactive oxygen species generated by the photosensitiser, such as hydroxyl radicals, singlet oxygen or superoxide ion. Reactions of the excited sensitizer can involve electron or hydrogen transfer, usually with a reducing substrate (Type I reaction) or interaction with oxygen (Type II reaction). These various alternative processes and reactions can be controlled by choice of specific reaction conditions, leading to a wide range of products. A common example is the [4+2]-cycloaddition of singlet oxygen with a diene such as cyclopentadiene to yield an endoperoxide:

Polymerization
Terminal alkenes are precursors to polymers via processes termed polymerization. Some polymerizations are of great economic significance, as they generate the plastics polyethylene and polypropylene. Polymers from alkene are usually referred to as polyolefins although they contain no olefins. Polymerization can proceed via diverse mechanisms. Conjugated dienes such as buta-1,3-diene and isoprene (2-methylbuta-1,3-diene) also produce polymers, one example being natural rubber.

Allylic substitution
The presence of a C=C π bond in unsaturated hydrocarbons weakens the dissociation energy of the allylic C−H bonds. Thus, these groupings are susceptible to free radical substitution at these C-H sites as well as addition reactions at the C=C site. In the presence of radical initiators, allylic C-H bonds can be halogenated. The presence of two C=C bonds flanking one methylene, i.e., doubly allylic, results in particularly weak HC-H bonds. The high reactivity of these situations is the basis for certain free radical reactions, manifested in the chemistry of drying oils.

Metathesis
Alkenes undergo olefin metathesis, which cleaves and interchanges the substituents of the alkene. A related reaction is ethenolysis:

Metal complexation

 * [[Image:Ni(cod)2.png|thumb|right|220px|Structure of [[bis(cyclooctadiene)nickel(0)]], a metal–alkene complex]]

In transition metal alkene complexes, alkenes serve as ligands for metals. In this case, the π electron density is donated to the metal d orbitals. The stronger the donation is, the stronger the back bonding from the metal d orbital to π* anti-bonding orbital of the alkene. This effect lowers the bond order of the alkene and increases the C-C bond length. One example is the complex PtCl3(C2H4)]-. These complexes are related to the mechanisms of metal-catalyzed reactions of unsaturated hydrocarbons.

Industrial methods
Alkenes are produced by hydrocarbon cracking. Raw materials are mostly natural-gas condensate components (principally ethane and propane) in the US and Mideast and naphtha in Europe and Asia. Alkanes are broken apart at high temperatures, often in the presence of a zeolite catalyst, to produce a mixture of primarily aliphatic alkenes and lower molecular weight alkanes. The mixture is feedstock and temperature dependent, and separated by fractional distillation. This is mainly used for the manufacture of small alkenes (up to six carbons).

Related to this is catalytic dehydrogenation, where an alkane loses hydrogen at high temperatures to produce a corresponding alkene. This is the reverse of the catalytic hydrogenation of alkenes. This process is also known as reforming. Both processes are endothermic and are driven towards the alkene at high temperatures by entropy.

Catalytic synthesis of higher α-alkenes (of the type RCH=CH2) can also be achieved by a reaction of ethylene with the organometallic compound triethylaluminium in the presence of nickel, cobalt, or platinum.

Elimination reactions
One of the principal methods for alkene synthesis in the laboratory is the elimination reaction of alkyl halides, alcohols, and similar compounds. Most common is the β-elimination via the E2 or E1 mechanism. A commercially significant example is the production of vinyl chloride.

The E2 mechanism provides a more reliable β-elimination method than E1 for most alkene syntheses. Most E2 eliminations start with an alkyl halide or alkyl sulfonate ester (such as a tosylate or triflate). When an alkyl halide is used, the reaction is called a dehydrohalogenation. For unsymmetrical products, the more substituted alkenes (those with fewer hydrogens attached to the C=C) tend to predominate (see Zaitsev's rule). Two common methods of elimination reactions are dehydrohalogenation of alkyl halides and dehydration of alcohols. A typical example is shown below; note that if possible, the H is anti to the leaving group, even though this leads to the less stable Z-isomer.

Alkenes can be synthesized from alcohols via dehydration, in which case water is lost via the E1 mechanism. For example, the dehydration of ethanol produces ethylene:
 * CH3CH2OH  →  H2C=CH2 +  H2O

An alcohol may also be converted to a better leaving group (e.g., xanthate), so as to allow a milder syn-elimination such as the Chugaev elimination and the Grieco elimination. Related reactions include eliminations by β-haloethers (the Boord olefin synthesis) and esters (ester pyrolysis). A thioketone and a phosphite ester combined (the Corey-Winter olefination) or diphosphorus tetraiodide will deoxygenate glycols to alkenes.

Alkenes can be prepared indirectly from alkyl amines. The amine or ammonia is not a suitable leaving group, so the amine is first either alkylated (as in the Hofmann elimination) or oxidized to an amine oxide (the Cope reaction) to render a smooth elimination possible. The Cope reaction is a syn-elimination that occurs at or below 150 °C, for example:

The Hofmann elimination is unusual in that the less substituted (non-Zaitsev) alkene is usually the major product.

Alkenes are generated from α-halosulfones in the Ramberg–Bäcklund reaction, via a three-membered ring sulfone intermediate.

Synthesis from carbonyl compounds
Another important class of methods for alkene synthesis involves construction of a new carbon–carbon double bond by coupling or condensation of a carbonyl compound (such as an aldehyde or ketone) to a carbanion or its equivalent. Pre-eminent is the aldol condensation. Knoevenagel condensations are a related class of reactions that convert carbonyls into alkenes.Well-known methods are called olefinations. The Wittig reaction is illustrative, but other related methods are known, including the Horner–Wadsworth–Emmons reaction. The Wittig reaction involves reaction of an aldehyde or ketone with a Wittig reagent (or phosphorane) of the type Ph3P=CHR to produce an alkene and Ph3P=O. The Wittig reagent is itself prepared easily from triphenylphosphine and an alkyl halide.

Related to the Wittig reaction is the Peterson olefination, which uses silicon-based reagents in place of the phosphorane. This reaction allows for the selection of E- or Z-products. If an E-product is desired, another alternative is the Julia olefination, which uses the carbanion generated from a phenyl sulfone. The Takai olefination based on an organochromium intermediate also delivers E-products. A titanium compound, Tebbe's reagent, is useful for the synthesis of methylene compounds; in this case, even esters and amides react.

A pair of ketones or aldehydes can be deoxygenated to generate an alkene. Symmetrical alkenes can be prepared from a single aldehyde or ketone coupling with itself, using titanium metal reduction (the McMurry reaction). If different ketones are to be coupled, a more complicated method is required, such as the Barton–Kellogg reaction.

A single ketone can also be converted to the corresponding alkene via its tosylhydrazone, using sodium methoxide (the Bamford–Stevens reaction) or an alkyllithium (the Shapiro reaction).

Synthesis from alkenes
The formation of longer alkenes via the step-wise polymerisation of smaller ones is appealing, as ethylene (the smallest alkene) is both inexpensive and readily available, with hundreds of millions of tonnes produced annually. The Ziegler–Natta process allows for the formation of very long chains, for instance those used for polyethylene. Where shorter chains are wanted, as they for the production of surfactants, then processes incorporating a olefin metathesis step, such as the Shell higher olefin process are important. Olefin metathesis is also used commercially for the interconversion of ethylene and 2-butene to propylene. Rhenium- and molybdenum-containing heterogeneous catalysis are used in this process:
 * CH2=CH2 +  CH3CH=CHCH3   →   2 CH2=CHCH3

Transition metal catalyzed hydrovinylation is another important alkene synthesis process starting from alkene itself. It involves the addition of a hydrogen and a vinyl group (or an alkenyl group) across a double bond.

From alkynes
Reduction of alkynes is a useful method for the stereoselective synthesis of disubstituted alkenes. If the cis-alkene is desired, hydrogenation in the presence of Lindlar's catalyst (a heterogeneous catalyst that consists of palladium deposited on calcium carbonate and treated with various forms of lead) is commonly used, though hydroboration followed by hydrolysis provides an alternative approach. Reduction of the alkyne by sodium metal in liquid ammonia gives the trans-alkene.

For the preparation multisubstituted alkenes, carbometalation of alkynes can give rise to a large variety of alkene derivatives.

Rearrangements and related reactions
Alkenes can be synthesized from other alkenes via rearrangement reactions. Besides olefin metathesis (described above), many pericyclic reactions can be used such as the ene reaction and the Cope rearrangement.

In the Diels–Alder reaction, a cyclohexene derivative is prepared from a diene and a reactive or electron-deficient alkene.

Application
Unsaturated hydrocarbons are widely used to produce plastics, medicines, and other useful materials.

Natural occurrence
Alkenes are prevalent in nature. Plants are the main natural source of alkenes in the form of terpenes. Many of the most vivid natural pigments are terpenes; e.g. lycopene (red in tomatoes), carotene (orange in carrots), and xanthophylls (yellow in egg yolk). The simplest of all alkenes, ethylene is a signaling molecule that influences the ripening of plants.

IUPAC Nomenclature
Although the nomenclature is not followed widely, according to IUPAC, an alkene is an acyclic hydrocarbon with just one double bond between carbon atoms. Olefins comprise a larger collection of cyclic and acyclic alkenes as well as dienes and polyenes.

To form the root of the IUPAC names for straight-chain alkenes, change the -an- infix of the parent to -en-. For example, CH3-CH3 is the alkane ethANe. The name of CH2=CH2 is therefore ethENe.

For straight-chain alkenes with 4 or more carbon atoms, that name does not completely identify the compound. For those cases, and for branched acyclic alkenes, the following rules apply:
 * 1) Find the longest carbon chain in the molecule. If that chain does not contain the double bond, name the compound according to the alkane naming rules.  Otherwise:
 * 2) Number the carbons in that chain starting from the end that is closest to the double bond.
 * 3) Define the location k of the double bond as being the number of its first carbon.
 * 4) Name the side groups (other than hydrogen) according to the appropriate rules.
 * 5) Define the position of each side group as the number of the chain carbon it is attached to.
 * 6) Write the position and name of each side group.
 * 7) Write the names of the alkane with the same chain, replacing the "-ane" suffix by "k-ene".

The position of the double bond is often inserted before the name of the chain (e.g. "2-pentene"), rather than before the suffix ("pent-2-ene").

The positions need not be indicated if they are unique. Note that the double bond may imply a different chain numbering than that used for the corresponding alkane: C–– is "2,2-dimethyl pentane", whereas C–= is "3,3-dimethyl 1-pentene".

More complex rules apply for polyenes and cycloalkenes.

Cis–trans isomerism
If the double bond of an acyclic mono-ene is not the first bond of the chain, the name as constructed above still does not completely identify the compound, because of cis–trans isomerism. Then one must specify whether the two single C–C bonds adjacent to the double bond are on the same side of its plane, or on opposite sides. For monoalkenes, the configuration is often indicated by the prefixes cis- (from Latin "on this side of") or trans- ("across", "on the other side of") before the name, respectively; as in cis-2-pentene or trans-2-butene.

More generally, cis–trans isomerism will exist if each of the two carbons of in the double bond has two different atoms or groups attached to it. Accounting for these cases, the IUPAC recommends the more general E–Z notation, instead of the cis and trans prefixes. This notation considers the group with highest CIP priority in each of the two carbons. If these two groups are on opposite sides of the double bond's plane, the configuration is labeled E (from the German entgegen meaning "opposite"); if they are on the same side, it is labeled Z (from German zusammen, "together"). This labeling may be taught with mnemonic "Z means 'on ze zame zide'".

Groups containing C=C double bonds
IUPAC recognizes two names for hydrocarbon groups containing carbon–carbon double bonds, the vinyl group and the allyl group.

Nomenclature links

 * Rule A-3. Unsaturated Compounds and Univalent Radicals IUPAC Blue Book.
 * Rule A-4. Bivalent and Multivalent Radicals IUPAC Blue Book.
 * Rules A-11.3, A-11.4, A-11.5 Unsaturated monocyclic hydrocarbons and substituents IUPAC Blue Book.
 * Rule A-23. Hydrogenated Compounds of Fused Polycyclic Hydrocarbons IUPAC Blue Book.

title: Alkene


text:
Allenes

In organic chemistry, allenes are organic compounds in which one carbon atom has double bonds with each of its two adjacent carbon atoms (R2C\dC\dCR2, where R is H or some organyl group). Allenes are classified as cumulated dienes. The parent compound of this class is propadiene (H2C\dC\dCH2), which is itself also called allene. A group of the structure R2C\dC\dCR\s is called allenyl, while a substituent attached to an allene is referred to as an allenic substituent (R is H or some alkyl group). In analogy to allylic and propargylic, a substituent attached to a saturated carbon α (i.e., directly adjacent) to an allene is referred to as an allenylic substituent. While allenes have two consecutive ('cumulated') double bonds, compounds with three or more cumulated double bonds are called cumulenes.

History
For many years, allenes were viewed as curiosities but thought to be synthetically useless and difficult to prepare and to work with. Reportedly, the first synthesis of an allene, glutinic acid, was performed in an attempt to prove the non-existence of this class of compounds. The situation began to change in the 1950s, and more than 300 papers on allenes have been published in 2012 alone. These compounds are not just interesting intermediates but synthetically valuable targets themselves; for example, over 150 natural products are known with an allene or cumulene fragment.

Geometry
The central carbon atom of allenes forms two sigma bonds and two pi bonds. The central carbon atom is sp-hybridized, and the two terminal carbon atoms are sp2-hybridized. The bond angle formed by the three carbon atoms is 180°, indicating linear geometry for the central carbon atom. The two terminal carbon atoms are planar, and these planes are twisted 90° from each other. The structure can also be viewed as an "extended tetrahedral" with a similar shape to methane, an analogy that is continued into the stereochemical analysis of certain derivative molecules.

Symmetry
The symmetry and isomerism of allenes has long fascinated organic chemists. For allenes with four identical substituents, there exist two twofold axes of rotation through the central carbon atom, inclined at 45° to the CH2 planes at either end of the molecule. The molecule can thus be thought of as a two-bladed propeller. A third twofold axis of rotation passes through the C=C=C bonds, and there is a mirror plane passing through both CH2 planes. Thus this class of molecules belong to the D2d point group. Because of the symmetry, an unsubstituted allene has no net dipole moment, that is, it is a non-polar molecule.

An allene with two different substituents on each of the two carbon atoms will be chiral because there will no longer be any mirror planes. The chirality of these types of allenes was first predicted in 1875 by Jacobus Henricus van 't Hoff, but not proven experimentally until 1935. Where A has a greater priority than B according to the Cahn–Ingold–Prelog priority rules, the configuration of the axial chirality can be determined by considering the substituents on the front atom followed by the back atom when viewed along the allene axis. For the back atom, only the group of higher priority need be considered.

Chiral allenes have been recently used as building blocks in the construction of organic materials with exceptional chiroptical properties. There are a few examples of drug molecule having an allene system in their structure. Mycomycin, an antibiotic with tuberculostatic properties, is a typical example. This drug exhibits enantiomerism due to the presence of a suitably substituted allene system.

Although the semi-localized textbook σ-π separation model describes the bonding of allene using a pair of localized orthogonal π orbitals, the full molecular orbital description of the bonding is more subtle. The symmetry-correct doubly-degenerate HOMOs of allene (adapted to the D2d point group) can either be represented by a pair of orthogonal MOs or as twisted helical linear combinations of these orthogonal MOs. The symmetry of the system and the degeneracy of these orbitals imply that both descriptions are correct (in the same way that there are infinitely many ways to depict the doubly-degenerate HOMOs and LUMOs of benzene that correspond to different choices of eigenfunctions in a two-dimensional eigenspace). However, this degeneracy is lifted in substituted allenes, and the helical picture becomes the only symmetry-correct description for the HOMO and HOMO–1 of the C2-symmetric 1,3-dimethylallene. This qualitative MO description extends to higher odd-carbon cumulenes (e.g., 1,2,3,4-pentatetraene).

Chemical and spectral properties
Allenes differ considerably from other alkenes in terms of their chemical properties. Compared to isolated and conjugated dienes, they are considerably less stable: comparing the isomeric pentadienes, the allenic 1,2-pentadiene has a heat of formation of 33.6 kcal/mol, compared to 18.1 kcal/mol for (E)-1,3-pentadiene and 25.4 kcal/mol for the isolated 1,4-pentadiene.

The C–H bonds of allenes are considerably weaker and more acidic compared to typical vinylic C–H bonds: the bond dissociation energy is 87.7 kcal/mol (compared to 111 kcal/mol in ethylene), while the gas-phase acidity is 381 kcal/mol (compared to 409 kcal/mol for ethylene ), making it slightly more acidic than the propargylic C–H bond of propyne (382 kcal/mol).

The 13C NMR spectrum of allenes is characterized by the signal of the sp-hybridized carbon atom, resonating at a characteristic 200-220 ppm. In contrast, the sp2-hybridized carbon atoms resonate around 80 ppm in a region typical for alkyne and nitrile carbon atoms, while the protons of a CH2 group of a terminal allene resonate at around 4.5 ppm — somewhat upfield of a typical vinylic proton.

Allenes possess a rich cycloaddition chemistry, including both [4+2] and [2+2] modes of addition, as well as undergoing formal cycloaddition processes catalyzed by transition metals. Allenes also serve as substrates for transition metal catalyzed hydrofunctionalization reactions.

Synthesis
Although allenes often require specialized syntheses, the parent allene, propadiene is produced industrially on a large scale as an equilibrium mixture with propyne:

This mixture, known as MAPP gas, is commercially available. At 298 K, the ΔG° of this reaction is –1.9 kcal/mol, corresponding to Keq = 24.7.

The first allene to be synthesized was penta-2,3-dienedioic acid, which was prepared by Burton and Pechmann in 1887. However, the structure was only correctly identified in 1954.

Laboratory methods for the formation of allenes include: The chemistry of allenes has been reviewed in a number of books and journal articles. Some key approaches towards allenes are outlined in the following scheme:
 * from geminal dihalocyclopropanes and organolithium compounds (or metallic sodium or magnesium) in the Skattebøl rearrangement (Doering–LaFlamme allene synthesis) via rearrangement of cyclopropylidene carbenes/carbenoids
 * from reaction of certain terminal alkynes with formaldehyde, copper(I) bromide, and added base (Crabbé–Ma allene synthesis)
 * from propargylic halides by SN2′ displacement by an organocuprate
 * from dehydrohalogenation of certain dihalides
 * from reaction of a triphenylphosphinyl ester with an acid halide, a Wittig reaction accompanied by dehydrohalogenation
 * from propargylic alcohols via the Myers allene synthesis protocol—a stereospecific process
 * from metalation of allene or substituted allenes with BuLi and reaction with electrophiles (RX, R3SiX, D2O, etc.)

One of the older methods is the Skattebøl rearrangement (also called the Doering–Moore–Skattebøl or Doering–LaFlamme  rearrangement), in which a gem-dihalocyclopropane 3 is treated with an organolithium compound (or dissolving metal) and the presumed intermediate rearranges into an allene either directly or via carbene-like species. Notably, even strained allenes can be generated by this procedure. Modifications involving leaving groups of different nature are also known. Arguably, the most convenient modern method of allene synthesis is by sigmatropic rearrangement of propargylic substrates. Johnson–Claisen and Ireland–Claisen rearrangements of ketene acetals 4 have been used a number of times to prepare allenic esters and acids. Reactions of vinyl ethers 5 (the Saucy–Marbet rearrangement) give allene aldehydes, while propargylic sulfenates 6 give allene sulfoxides. Allenes can also be prepared by nucleophilic substitution in 9 and 10 (nucleophile Nu− can be a hydride anion), 1,2-elimination from 8, proton transfer in 7, and other, less general, methods.

Use and occurrence
Allene itself is the most commonly used member of this family; it exists in equilibrium with propyne as a component of MAPP gas.

Research
The reactivity of substituted allenes has been well explored.

The two π-bonds are located at the 90° angle to each other, and thus require a reagent to approach from somewhat different directions. With an appropriate substitution pattern, allenes exhibit axial chirality as predicted by van’t Hoff as early as 1875. Protonation of allenes gives cations 11 that undergo further transformations. Reactions with soft electrophiles (e.g. Br+) deliver positively charged onium ions 13. Transition-metal-catalysed reactions proceed via allylic intermediates 15 and have attracted significant interest in recent years. Numerous cycloadditions are also known, including [4+2]-, (2+1)-, and [2+2]-variants, which deliver, e.g., 12, 14, and 16, respectively.

Occurrence
Numerous natural products contain the allene functional group. Noteworthy are the pigments fucoxanthin and peridinin. Little is known about the biosynthesis, although it is conjectured that they are often generated from alkyne precursors.

Allenes serve as ligands in organometallic chemistry. A typical complex is Pt(η2-allene)(PPh3)2. Ni(0) reagents catalyze the cyclooligomerization of allene. Using a suitable catalyst (e.g. Wilkinson's catalyst), it is possible to reduce just one of the double bonds of an allene.

Delta convention
Many rings or ring systems are known by semisystematic names that assume a maximum number of noncumulative bonds. To unambiguously specify derivatives that include cumulated bonds (and hence fewer hydrogen atoms than would be expected from the skeleton), a lowercase delta may be used with a subscript indicating the number of cumulated double bonds from that atom, e.g. 8δ2-benzocyclononene. This may be combined with the λ-convention for specifying nonstandard valency states, e.g. 2λ4δ2,5λ4δ2-thieno[3,4-c]thiophene.

title: Allenes


text:
Alkyne

Acetylene

Propyne

1-Butyne

In organic chemistry, an alkyne is an unsaturated hydrocarbon containing at least one carbon—carbon triple bond. The simplest acyclic alkynes with only one triple bond and no other functional groups form a homologous series with the general chemical formula C_{n}H_{2n-2}. Alkynes are traditionally known as acetylenes, although the name acetylene also refers specifically to C2H2, known formally as ethyne using IUPAC nomenclature. Like other hydrocarbons, alkynes are generally hydrophobic.

Structure and bonding
In acetylene, the H–C≡C bond angles are 180°. By virtue of this bond angle, alkynes are rod-like. Correspondingly, cyclic alkynes are rare. Benzyne cannot be isolated. The C≡C bond distance of 118 picometers (for C2H2) is much shorter than the C=C distance in alkenes (132 pm, for C2H4) or the C–C bond in alkanes (153 pm).

 * Alkyne General Formulae V.2.png, e, the naturally occurring 1-phenylhepta-1,3,5-triyne, and f, the strained cycloheptyne. Triple bonds are highlighted blue .]]

The triple bond is very strong with a bond strength of 839 kJ/mol. The sigma bond contributes 369 kJ/mol, the first pi bond contributes 268 kJ/mol. and the second pi bond 202 kJ/mol. Bonding is usually discussed in the context of molecular orbital theory, which recognizes the triple bond as arising from overlap of s and p orbitals. In the language of valence bond theory, the carbon atoms in an alkyne bond are sp hybridized: they each have two unhybridized p orbitals and two sp hybrid orbitals. Overlap of an sp orbital from each atom forms one sp–sp sigma bond. Each p orbital on one atom overlaps one on the other atom, forming two pi bonds, giving a total of three bonds. The remaining sp orbital on each atom can form a sigma bond to another atom, for example to hydrogen atoms in the parent acetylene. The two sp orbitals project on opposite sides of the carbon atom.

Terminal and internal alkynes
Internal alkynes feature carbon substituents on each acetylenic carbon. Symmetrical examples include diphenylacetylene and 3-hexyne. They may also be asymmetrical, such as in 2-pentyne.

Terminal alkynes have the formula RC2H. An example is methylacetylene (propyne using IUPAC nomenclature). They are often prepared by alkylation of monosodium acetylide. Terminal alkynes, like acetylene itself, are mildly acidic, with pKa values of around 25. They are far more acidic than alkenes and alkanes, which have pKa values of around 40 and 50, respectively. The acidic hydrogen on terminal alkynes can be replaced by a variety of groups resulting in halo-, silyl-, and alkoxoalkynes. The carbanions generated by deprotonation of terminal alkynes are called acetylides.

Naming alkynes
In systematic chemical nomenclature, alkynes are named with the Greek prefix system without any additional letters. Examples include ethyne or octyne. In parent chains with four or more carbons, it is necessary to say where the triple bond is located. For octyne, one can either write 3-octyne or oct-3-yne when the bond starts at the third carbon. The lowest number possible is given to the triple bond. When no superior functional groups are present, the parent chain must include the triple bond even if it is not the longest possible carbon chain in the molecule. Ethyne is commonly called by its trivial name acetylene.

In chemistry, the suffix -yne is used to denote the presence of a triple bond. In organic chemistry, the suffix often follows IUPAC nomenclature. However, inorganic compounds featuring unsaturation in the form of triple bonds may be denoted by substitutive nomenclature with the same methods used with alkynes (i.e. the name of the corresponding saturated compound is modified by replacing the "-ane" ending with "-yne"). "-diyne" is used when there are two triple bonds, and so on. The position of unsaturation is indicated by a numerical locant immediately preceding the "-yne" suffix, or 'locants' in the case of multiple triple bonds. Locants are chosen so that the numbers are low as possible. "-yne" is also used as a suffix to name substituent groups that are triply bound to the parent compound.

Sometimes a number between hyphens is inserted before it to state which atoms the triple bond is between. This suffix arose as a collapsed form of the end of the word "acetylene". The final "-e" disappears if it is followed by another suffix that starts with a vowel.

Structural isomerism
Alkynes having four or more carbon atoms can form different structural isomers by having the triple bond in different positions or having some of the carbon atoms be substituents rather than part of the parent chain. Other non-alkyne structural isomers are also possible.
 * C2H2: acetylene only
 * C3H4: propyne only
 * C4H6: 2 isomers: 1-butyne, and 2-butyne
 * C5H8: 3 isomers: 1-pentyne, 2-pentyne, and 3-methyl-1-butyne
 * C6H10: 7 isomers: 1-hexyne, 2-hexyne, 3-hexyne, 4-methyl-1-pentyne, 4-methyl-2-pentyne, 3-methyl-1-pentyne, 3,3-dimethyl-1-butyne

Cracking
Commercially, the dominant alkyne is acetylene itself, which is used as a fuel and a precursor to other compounds, e.g., acrylates. Hundreds of millions of kilograms are produced annually by partial oxidation of natural gas:

Propyne, also industrially useful, is also prepared by thermal cracking of hydrocarbons.

Dehydrohalogenation and related reactions
Alkynes are prepared from 1,1- and 1,2-dihaloalkanes by double dehydrohalogenation. The reaction provides a means to generate alkynes from alkenes, which are first halogenated and then dehydrohalogenated. For example, phenylacetylene can be generated from styrene by bromination followed by treatment of the resulting of styrene dibromide with sodium amide in ammonia:

 * Phenylacetylene prepn.png

Via the Fritsch–Buttenberg–Wiechell rearrangement, alkynes are prepared from vinyl bromides. Alkynes can be prepared from aldehydes using the Corey–Fuchs reaction and from aldehydes or ketones by the Seyferth–Gilbert homologation.

Vinyl halides are susceptible to dehydrohalogenation.

Reactions, including applications
Featuring a reactive functional group, alkynes participate in many organic reactions. Such use was pioneered by Ralph Raphael, who in 1955 wrote the first book describing their versatility as intermediates in synthesis.

Hydrogenation
Being more unsaturated than alkenes, alkynes characteristically undergo reactions that show that they are "doubly unsaturated". Alkynes are capable of adding two equivalents of H2, whereas an alkene adds only one equivalent. Depending on catalysts and conditions, alkynes add one or two equivalents of hydrogen. Partial hydrogenation, stopping after the addition of only one equivalent to give the alkene, is usually more desirable since alkanes are less useful: The largest scale application of this technology is the conversion of acetylene to ethylene in refineries (the steam cracking of alkanes yields a few percent acetylene, which is selectively hydrogenated in the presence of a palladium/silver catalyst). For more complex alkynes, the Lindlar catalyst is widely recommended to avoid formation of the alkane, for example in the conversion of phenylacetylene to styrene. Similarly, halogenation of alkynes gives the alkene dihalides or alkyl tetrahalides:

The addition of one equivalent of H2 to internal alkynes gives cis-alkenes.

Addition of halogens and related reagents
Alkynes characteristically are capable of adding two equivalents of halogens and hydrogen halides.

The addition of nonpolar E\sH bonds across C\tC is general for silanes, boranes, and related hydrides. The hydroboration of alkynes gives vinylic boranes which oxidize to the corresponding aldehyde or ketone. In the thiol-yne reaction the substrate is a thiol.

Addition of hydrogen halides has long been of interest. In the presence of mercuric chloride as a catalyst, acetylene and hydrogen chloride react to give vinyl chloride. While this method has been abandoned in the West, it remains the main production method in China.

Hydration
The hydration reaction of acetylene gives acetaldehyde. The reaction proceeds by formation of vinyl alcohol, which tautomerizes to form the aldehyde. This reaction was once a major industrial process but it has been displaced by the Wacker process. This reaction occurs in nature, the catalyst being acetylene hydratase.

Hydration of phenylacetylene gives acetophenone:

(Ph3P)AuCH3 catalyzes hydration of 1,8-nonadiyne to 2,8-nonanedione:

Tautomerism
Terminal alkyl alkynes exhibit tautomerism. Propyne exists in equilibrium with propadiene:

Cycloadditions and oxidation
Alkynes undergo diverse cycloaddition reactions. The Diels–Alder reaction with 1,3-dienes gives 1,4-cyclohexadienes. This general reaction has been extensively developed. Electrophilic alkynes are especially effective dienophiles. The "cycloadduct" derived from the addition of alkynes to 2-pyrone eliminates carbon dioxide to give the aromatic compound. Other specialized cycloadditions include multicomponent reactions such as alkyne trimerisation to give aromatic compounds and the [2+2+1]-cycloaddition of an alkyne, alkene and carbon monoxide in the Pauson–Khand reaction. Non-carbon reagents also undergo cyclization, e.g. azide alkyne Huisgen cycloaddition to give triazoles. Cycloaddition processes involving alkynes are often catalyzed by metals, e.g. enyne metathesis and alkyne metathesis, which allows the scrambling of carbyne (RC) centers:

Oxidative cleavage of alkynes proceeds via cycloaddition to metal oxides. Most famously, potassium permanganate converts alkynes to a pair of carboxylic acids.

Reactions specific for terminal alkynes
Terminal alkynes are readily converted to many derivatives, e.g. by coupling reactions and condensations. Via the condensation with formaldehyde and acetylene is produced butynediol:

In the Sonogashira reaction, terminal alkynes are coupled with aryl or vinyl halides:
 * Sonogashira reaction scheme ACS.png

This reactivity exploits the fact that terminal alkynes are weak acids, whose typical pKa values around 25 place them between that of ammonia (35) and ethanol (16):

where MX = NaNH2, LiBu, or RMgX.

The reactions of alkynes with certain metal cations, e.g. Ag+ and Cu+ also gives acetylides. Thus, few drops of diamminesilver(I) hydroxide (Ag(NH3)2OH) reacts with terminal alkynes signaled by formation of a white precipitate of the silver acetylide. This reactivity is the basis of alkyne coupling reactions, including the Cadiot–Chodkiewicz coupling, Glaser coupling, and the Eglinton coupling shown below:

In the Favorskii reaction and in alkynylations in general, terminal alkynes add to carbonyl compounds to give the hydroxyalkyne.

Metal complexes
Alkynes form complexes with transition metals. Such complexes occur also in metal catalyzed reactions of alkynes such as alkyne trimerization. Terminal alkynes, including acetylene itself, react with water to give aldehydes. The transformation typically requires metal catalysts to give this anti-Markovnikov addition result.

Alkynes in nature and medicine
According to Ferdinand Bohlmann, the first naturally occurring acetylenic compound, dehydromatricaria ester, was isolated from an Artemisia species in 1826. In the nearly two centuries that have followed, well over a thousand naturally occurring acetylenes have been discovered and reported. Polyynes, a subset of this class of natural products, have been isolated from a wide variety of plant species, cultures of higher fungi, bacteria, marine sponges, and corals. Some acids like tariric acid contain an alkyne group. Diynes and triynes, species with the linkage RC≡C–C≡CR′ and RC≡C–C≡C–C≡CR′ respectively, occur in certain plants (Ichthyothere, Chrysanthemum, Cicuta, Oenanthe and other members of the Asteraceae and Apiaceae families). Some examples are cicutoxin, oenanthotoxin, and falcarinol. These compounds are highly bioactive, e.g. as nematocides. 1-Phenylhepta-1,3,5-triyne is illustrative of a naturally occurring triyne.

Alkynes occur in some pharmaceuticals, including the contraceptive noretynodrel. A carbon–carbon triple bond is also present in marketed drugs such as the antiretroviral Efavirenz and the antifungal Terbinafine. Molecules called ene-diynes feature a ring containing an alkene ("ene") between two alkyne groups ("diyne"). These compounds, e.g. calicheamicin, are some of the most aggressive antitumor drugs known, so much so that the ene-diyne subunit is sometimes referred to as a "warhead". Ene-diynes undergo rearrangement via the Bergman cyclization, generating highly reactive radical intermediates that attack DNA within the tumor.

title: Alkyne


text:
AbiWord

AbiWord is a free and open-source word processor. It is written in C++ and since version 3 it is based on GTK+ 3. The name "AbiWord" is derived from the root of the Spanish word "abierto", meaning "open".

AbiWord was originally started by SourceGear Corporation as the first part of a proposed AbiSuite but was adopted by open source developers after SourceGear changed its business focus and ceased development. It now runs on Linux, ReactOS, Solaris, AmigaOS 4.0 (through its Cygwin X11 engine), MeeGo (on the Nokia N9 smartphone), Maemo (on the Nokia N810), QNX and other operating systems. Development of a version for Microsoft Windows has temporarily ended due to lack of maintainers (the latest released versions are 2.8.6 and 2.9.4 beta).

The macOS port has remained on version 2.4 since 2005, although the current version does run non-natively on macOS through XQuartz.

AbiWord is part of the AbiSource project which develops a number of office-related technologies.

Features
AbiWord supports both basic word processing features such as lists, indents and character formats, and more sophisticated features including tables, styles, page headers and footers, footnotes, templates, multiple views, page columns, spell checking, and grammar checking. The Presentation view of AbiWord, which permits easy display of presentations created in AbiWord on "screen-sized" pages, is another feature not often found in word processors.

Interface
AbiWord generally works similarly to classic versions (pre-Office 2007) of Microsoft Word, as direct ease of migration was a high priority early goal. While many interface similarities remain, cloning the Word interface is no longer a top priority. The interface is intended to follow user interface guidelines for each respective platform.

Collaboration
AbiWord allows users to share and collaborate on documents in a similar manner to Google Docs, using a system known as GOCollab. Users can collaborate using a varitety of different protocols including TCP and XMPP, and formerly over AbiCollab.net, a web based service that facilitated collaboration between users.

File formats
AbiWord comes with several import and export filters providing partial support for such formats as HTML, Microsoft Word (.doc), Office Open XML (.docx), OpenDocument Text (.odt), Rich Text Format (.rtf), and text documents (.txt). LaTeX is supported for export only. Plug-in filters are available to deal with many other formats, notably WordPerfect documents. The native file format, .abw, uses XML, so as to mitigate vendor lock-in concerns with respect to interoperability and digital archiving.

Grammar checking
The AbiWord project includes a US English-only grammar checking plugin using Link Grammar. AbiWord had grammar checking before any other open source word processor, although a grammar checker was later added to OpenOffice.org. Link Grammar is both a theory of syntax and an open source parser which is now developed by the AbiWord project.

title: AbiWord


text:
Ames test

The Ames test is a widely employed method that uses bacteria to test whether a given chemical can cause mutations in the DNA of the test organism. More formally, it is a biological assay to assess the mutagenic potential of chemical compounds. A positive test indicates that the chemical is mutagenic and therefore may act as a carcinogen, because cancer is often linked to mutation. The test serves as a quick and convenient assay to estimate the carcinogenic potential of a compound because standard carcinogen assays on mice and rats are time-consuming (taking two to three years to complete) and expensive. However, false-positives and false-negatives are known.

The procedure was described in a series of papers in the early 1970s by Bruce Ames and his group at the University of California, Berkeley.

General procedure
The Ames test uses several strains of the bacterium Salmonella typhimurium that carry mutations in genes involved in histidine synthesis. These strains are auxotrophic mutants, i.e. they require histidine for growth, but cannot produce it. The method tests the capability of the tested substance in creating mutations that result in a return to a "prototrophic" state, so that the cells can grow on a histidine-free medium.

The tester strains are specially constructed to detect either frameshift (e.g. strains TA-1537 and TA-1538) or point (e.g. strain TA-1531) mutations in the genes required to synthesize histidine, so that mutagens acting via different mechanisms may be identified. Some compounds are quite specific, causing reversions in just one or two strains. The tester strains also carry mutations in the genes responsible for lipopolysaccharide synthesis, making the cell wall of the bacteria more permeable, and in the excision repair system to make the test more sensitive.

Larger organisms like mammals have metabolic processes that could potentially turn a chemical considered not mutagenic into one that is or one that is considered mutagenic into one that is not. Therefore, to more effectively test a chemical compound's mutagenicity in relation to larger organisms, rat liver enzymes can be added in an attempt to replicate the metabolic processes' effect on the compound being tested in the Ames Test. Rat liver extract is optionally added to simulate the effect of metabolism, as some compounds, like benzo[a]pyrene, are not mutagenic themselves but their metabolic products are.

The bacteria are spread on an agar plate with small amount of histidine. This small amount of histidine in the growth medium allows the bacteria to grow for an initial time and have the opportunity to mutate. When the histidine is depleted only bacteria that have mutated to gain the ability to produce its own histidine will survive. The plate is incubated for 48 hours. The mutagenicity of a substance is proportional to the number of colonies observed.

Ames test and carcinogens
Mutagens identified via Ames test are also possible carcinogens, and early studies by Ames showed that 90% of known carcinogens may be identified via this test. Later studies however showed identification of 50–70% of known carcinogens. The test was used to identify a number of compounds previously used in commercial products as potential carcinogens. Examples include tris(2,3-dibromopropyl)phosphate, which was used as a flame retardant in plastic and textiles such as children's sleepwear, and furylfuramide which was used as an antibacterial additive in food in Japan in the 1960s and 1970s. Furylfuramide in fact had previously passed animal tests, but more vigorous tests after its identification in the Ames test showed it to be carcinogenic. Their positive tests resulted in those chemicals being withdrawn from use in consumer products.

One interesting result from the Ames test is that the dose response curve using varying concentrations of the chemical is almost always linear, indicating that there is no threshold concentration for mutagenesis. It therefore suggests that, as with radiation, there may be no safe threshold for chemical mutagens or carcinogens. However, some have proposed that organisms could tolerate low levels of mutagens due to protective mechanisms such as DNA repair, and thus a threshold may exist for certain chemical mutagens. Bruce Ames himself argued against linear dose-response extrapolation from the high dose used in carcinogenesis tests in animal systems to the lower dose of chemicals normally encountered in human exposure, as the results may be false positives due to mitogenic response caused by the artificially high dose of chemicals used in such tests. He also cautioned against the "hysteria over tiny traces of chemicals that may or may not cause cancer", that "completely drives out the major risks you should be aware of".

The Ames test is often used as one of the initial screens for potential drugs to weed out possible carcinogens, and it is one of the eight tests required under the Pesticide Act (USA) and one of the six tests required under the Toxic Substances Control Act (USA).

Limitations
Salmonella typhimurium is a prokaryote, therefore it is not a perfect model for humans. Rat liver S9 fraction is used to mimic the mammalian metabolic conditions so that the mutagenic potential of metabolites formed by a parent molecule in the hepatic system can be assessed; however, there are differences in metabolism between humans and rats that can affect the mutagenicity of the chemicals being tested. The test may therefore be improved by the use of human liver S9 fraction; its use was previously limited by its availability, but it is now available commercially and therefore may be more feasible. An adapted in vitro model has been made for eukaryotic cells, for example yeast.

Mutagens identified in the Ames test need not necessarily be carcinogenic, and further tests are required for any potential carcinogen identified in the test. Drugs that contain the nitrate moiety sometimes come back positive for Ames when they are indeed safe. The nitrate compounds may generate nitric oxide, an important signal molecule that can give a false positive. Nitroglycerin is an example that gives a positive Ames yet is still used in treatment today. Nitrates in food however may be reduced by bacterial action to nitrites which are known to generate carcinogens by reacting with amines and amides. Long toxicology and outcome studies are needed with such compounds to disprove a positive Ames test.

Fluctuation method
The Ames test was initially developed using agar plates (the plate incorporation technique), as described above. Since that time, an alternative to performing the Ames test has been developed, which is known as the "fluctuation method". This technique is the same in concept as the agar-based method, with bacteria being added to a reaction mixture with a small amount of histidine, which allows the bacteria to grow and mutate, returning to synthesize their own histidine. By including a pH indicator, the frequency of mutation is counted in microplates as the number of wells which have changed color (caused by a drop in pH due to metabolic processes of reproducing bacteria). As with the traditional Ames test, the sample is compared to the natural background rate of reverse mutation in order to establish the genotoxicity of a substance. The fluctuation method is performed entirely in liquid culture and is scored by counting the number of wells that turn yellow from purple in 96-well or 384-well microplates.

In the 96-well plate method the frequency of mutation is counted as the number of wells out of 96 which have changed color. The plates are incubated for up to five days, with mutated (yellow) colonies being counted each day and compared to the background rate of reverse mutation using established tables of significance to determine the significant differences between the background rate of mutation and that for the tested samples.

In the more scaled-down 384-well plate microfluctuation method the frequency of mutation is counted as the number of wells out of 48 which have changed color after 2 days of incubation. A test sample is assayed across 6 dose levels with concurrent zero-dose (background) and positive controls which all fit into one 384-well plate. The assay is performed in triplicates to provide statistical robustness. It uses the recommended OECD Guideline 471 tester strains (histidine auxotrophs and tryptophan auxotrophs).

The fluctuation method is comparable to the traditional pour plate method in terms of sensitivity and accuracy, however, it does have a number of advantages: it needs less test sample, it has a simple colorimetric endpoint, counting the number of positive wells out of possible 96 or 48 wells is much less time-consuming than counting individual colonies on an agar plate. Several commercial kits are available. Most kits have consumable components in a ready-to-use state, including lyophilized bacteria, and tests can be performed using multichannel pipettes. The fluctuation method also allows for testing higher volumes of aqueous samples (up to 75% v/v), increasing the sensitivity and extending its application to low-level environmental mutagens.

title: Ames test