Sex chromosome

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Sex_chromosome 

 

Human male XY chromosomes after G-banding

A sex chromosome (also referred to as an allosome, heterotypical chromosome, gonosome, heterochromosome,  or idiochromosome) is a chromosome that differs from an ordinary autosome in form, size, and behavior. The human sex chromosomes, a typical pair of mammal allosomes, determine the sex of an individual created in sexual reproduction. Autosomes differ from allosomes because autosomes appear in pairs whose members have the same form but differ from other pairs in a diploid cell, whereas members of an allosome pair may differ from one another and thereby determine sex.

Nettie Stevens and Edmund Beecher Wilson both independently discovered sex chromosomes in 1905. However, Stevens is credited for discovering them earlier than Wilson.

Differentiation

In humans, each cell nucleus contains 23 pairs of chromosomes, a total of 46 chromosomes. The first 22 pairs are called autosomes. Autosomes are homologous chromosomes i.e. chromosomes which contain the same genes (regions of DNA) in the same order along their chromosomal arms. The 23rd pair of chromosomes are called allosomes. These consist of two X chromosomes in most females, and an X chromosome and a Y chromosome in most males. Females therefore have 23 homologous chromosome pairs, while males have 22. The X and Y chromosomes have small regions of homology called pseudoautosomal regions.

The X chromosome is always present as the 23rd chromosome in the ovum, while either an X or Y chromosome may be present in an individual sperm. Early in female embryonic development, in cells other than egg cells, one of the X chromosomes is randomly and permanently partially deactivated: In some cells, the X chromosome inherited from the mother deactivates; in other cells, it’s the X chromosome inherited from the father. This ensures that both sexes always have exactly one functional copy of the X chromosome in each body cell. The deactivated X chromosome is silenced by repressive heterochromatin that compacts the DNA and prevents expression of most genes. This compaction is regulated by PRC2 (Polycomb Repressive Complex 2).

Sex determination

Main article: Sex-determination system

See also: Sexual differentiation in humans

All diploid organisms with allosome-determined sex get half of their allosomes from each of their parents. In most mammals, females are XX, and can pass along either of their Xs; since males are XY they can pass along either an X or a Y. Females in such species receive an X chromosome from each parent while males receive an X chromosome from their mother and a Y chromosome from their father. It is thus the male's sperm that determines the sex of each offspring in such species.

However, a small percentage of humans have a divergent sexual development, known as intersex. This can result from allosomes that are neither XX nor XY. It can also occur when two fertilized embryo fuse, producing a chimera that might contain two different sets of DNA one XX and the other XY. It could also result from exposure, often in utero, to chemicals that disrupt the normal conversion of the allosomes into sex hormones and further into the development of either ambiguous outer genitalia or internal organs.

There is a gene in the Y chromosome that has regulatory sequences that control genes that code for maleness, called the SRY gene. This gene produces a testis-determining factor ("TDF"), which initiates testis development in humans and other mammals. The SRY sequence's prominence in sex determination was discovered when the genetics of sex-reversed XX men (i.e. humans who possess biological male-traits but actually have XX allosomes) were studied. After examination, it was discovered that the difference between a typical XX individual (traditional female) and a sex-reversed XX man was that the typical individuals lacked the SRY gene. It is theorized that in sex-reversed XX men, the SRY mistakenly gets translocated to an X chromosome in the XX pair during meiosis.

Other vertebrates

Diverse mechanisms are involved in the determination of sex in animals. For mammals, sex determination is carried by the genetic contribution of the spermatozoon. Lower chordates, such as fish, amphibians and reptiles, have systems that are influenced by the environment. Fish and amphibians, for example, have genetic sex determination but their sex can also be influenced by externally available steroids and incubation temperature of eggs. In reptiles, only incubation temperature determines sex.

Plants

Many scientists argue that sex determination in plants is more complex than that in humans. This is because even flowering plants have a variety of mating systems, their sex determination primarily regulated by MADS-box genes. These genes code for proteins that form the sex organs in flowers.

Plant sex chromosomes are most common in bryophytes, relatively common in vascular plants and unknown in ferns and lycophytes. The diversity of plants is reflected in their sex-determination systems, which include XY and UV systems as well as many variants. Sex chromosomes have evolved independently across many plant groups. Recombination of chromosomes may lead to heterogamety before the development of sex chromosomes, or recombination may be reduced after sex chromosomes develop. Only a few pseudoautosomal regions normally remain once sex chromosomes are fully differentiated. When chromosomes do not recombine, neutral sequence divergences begin to accumulate, which has been used to estimate the age of sex chromosomes in various plant lineages. Even the oldest estimated divergence, in the liverwort Marchantia polymorpha, is more recent than mammal or bird divergence. Due to this recency, most plant sex chromosomes also have relatively small sex-linked regions. Current evidence does not support the existence of plant sex chromosomes more ancient than those of M. polymorpha.

The high prevalence of autopolyploidy in plants also impacts the structure of their sex chromosomes. Polyploidization can occur before and after the development of sex chromosomes. If it occurs after sex chromosomes are established, dosage should stay consistent between the sex chromosomes and autosomes, with minimal impact on sex differentiation. If it occurs before sex chromosomes become heteromorphic, as is likely in the octoploid red sorrel Rumex acetosella, sex is determined in a single XY system. In a more complicated system, the sandalwood species Viscum fischeri has X1X1X2X2 chromosomes in females, and X1X2Y chromosomes in males.

Sequence composition and evolution

Amplification of transposable elements, tandom repeats especially accumulation of long tandom repeats (LTR) retrotransposones are responsible for plant sex chromosome evolution. The insertion of retrotransposons is probably the major cause of y-chromosome expansion and plant genome size evolution. Retrotransposones contribute in size determination of sex chromosomes and its proliferation varies even in closely related species. LTR and tandom repeats play dominant role in the evolution of S. latifolia sex chromosomes. Athila is new family of retroelements, discovered in Arabidopsis thaliana, present in heterochromatin region only. Athila retroelements overrepresented in X but absent in Y while tandem repeats enriched in Y-chromosome. Some chloroplast sequences have also been identified in the Y-chromosome of S. latifolia. S. vulgaris has more retroelements in their sex chromosomes compare to S. latifolia. Microsatellite data shows that there is no significant difference between X and Y-chromosome microsatellites in both Silene species. This would conclude that microsatellites do not participate in Y-chromosome evolution. The portion of Y-chromosome that never recombine with X-chromosome faces selection reduction. This reduced selection leads to insertion of transposable elements and accumulation of deleterious mutation. The Y become larger and smaller than X due to insertion of retroelement and deletion of genetic material respectively. The genus Humulus is also used as model for the study of sex chromosomes evolution. Based on the phylogenetic topology distribution there are three regions on sex chromosomes. One region that stops recombining in the ancestor of H. lupulus, second that stops recombining in modern H. lupulus and the third region called pseudoautosomal region. H. lupulus is the rare case in plants in which Y is smaller than X, while its ancestor plant has the same size of both X and Y chromosomes. This size difference should be caused by deletion of genetic material in Y but that is not the case. This is because of complex dynamics like the larger size of X than Y-chromosome may be due to duplication or retrotransposition and size of Y remains same.

Non-vascular plants

Ferns and lycophytes have bisexual gametophytes, so there is no evidence for sex chromosomes. In the bryophytes, including liverworts, hornworts and mosses, sex chromosomes are common. The sex chromosomes in bryophytes affect what type of gamete is produced by the gametophyte, and there is wide diversity in gametophyte type. Unlike seed plants, where gametophytes are always unisexual, in bryophytes they may produce male, female, or both types of gamete.

Bryophytes most commonly employ a UV sex-determination system, where U produces female gametophytes and V produces male gametophytes. The U and V chromosomes are heteromorphic with U larger than V and are frequently both larger than the autosomes. There is variation even within this system, including UU/V and U/VV chromosome arrangements. In some bryophytes, microchromosomes have been found to co-occur with sex chromosomes and likely impact sex determination.

Gymnosperms

Dioecy is common among gymnosperms, found in an estimated 36% of species. However, heteromorphic sex chromosomes are relatively rare, with only 5 species known as of 2014. Five of these use an XY system, and one (Ginkgo biloba) uses a WZ system. Some gymnosperms, such as Johann's Pine (Pinus johannis), have homomorphic sex chromosomes that are almost indistinguishable through karyotyping.

Angiosperms

Cosexual angiosperms with either monoecious or hermaphroditic flowers do not have sex chromosomes. Angiosperms with separate sexes (dioecious) may use sex chromosomes or environmental flowers for sex determination. Cytogenetic data from about 100 angiosperm species showed heteromorphic sex chromosomes in approximately half, mostly taking the form of XY sex-determination systems. Their Y is typically larger, unlike in humans; however there is diversity among angiosperms. In the Poplar genus (Populus) some species have male heterogamety while others have female heterogamety. Sex chromosomes have arisen independently multiple times in angiosperms, from the monoecious ancestral condition. The move from a monoecious to dioecious system requires both male and female sterility mutations to be present in the population. Male sterility likely arises first as an adaptation to prevent selfing. Once male sterility has reached a certain prevalence, then female sterility may have a chance to arise and spread.

In the domesticated papaya (Carica papaya), three sex chromosomes are present, denoted as X, Y and Y^h. This corresponds with three sexes: females with XX chromosomes, males with XY, and hermaphrodites with XY^h . The hermaphrodite sex is estimated to have arisen only 4000 years ago, post-domestication of the plant. The genetic architecture suggests that either the Y chromosome has an X-inactivating gene, or that the Y^h chromosome has an X-activating gene.

Medical applications

Allosomes not only carry the genes that determine male and female traits, but also those for some other characteristics as well. Genes that are carried by either sex chromosome are said to be sex linked. Sex linked diseases are passed down through families through one of the X or Y chromosomes. Since usually men inherit Y chromosomes, they are the only ones to inherit Y-linked traits. Men and women can get the X-linked ones since both inherit X chromosomes.

An allele is either said to be dominant or recessive. Dominant inheritance occurs when an abnormal gene from one parent causes disease even though the matching gene from the other parent is normal. The abnormal allele dominates. Recessive inheritance is when both matching genes must be abnormal to cause disease. If only one gene in the pair is abnormal, the disease does not occur, or is mild. Someone who has one abnormal gene (but no symptoms) is called a carrier. A carrier can pass this abnormal gene to his or her children. X chromosome carry about 1500 genes, more than any other chromosome in the human body. Most of them code for something other than female anatomical traits. Many of the non-sex determining X-linked genes are responsible for abnormal conditions. The Y chromosome carries about 78 genes. Most of the Y chromosome genes are involved with essential cell house-keeping activities and sperm production. Only one of the Y chromosome genes, the SRY gene, is responsible for male anatomical traits. When any of the 9 genes involved in sperm production are missing or defective the result is usually very low sperm counts and infertility. Examples of mutations on the X chromosome include more common diseases such as the following:

• Color blindness or color vision deficiency is the inability or decreased ability to see color, or perceive color differences, under normal lighting conditions. Color blindness affects many individuals in the population. There is no actual blindness, but there is a deficiency of color vision. The most usual cause is a fault in the development of one or more sets of retinal cones that perceive color in light and transmit that information to the optic nerve. This type of color blindness is usually a sex-linked condition. The genes that produce photopigments are carried on the X chromosome; if some of these genes are missing or damaged, color blindness will be expressed in males with a higher probability than in females because males only have one X chromosome.
• Hemophilia refers to a group of bleeding disorders in which it takes a long time for the blood to clot. This is referred to as X-Linked recessive. Hemophilia is much more common in males than females because males are hemizygous. They only have one copy of the gene in question and therefore express the trait when they inherit one mutant allele. In contrast, a female must inherit two mutant alleles, a less frequent event since the mutant allele is rare in the population. X-linked traits are maternally inherited from carrier mothers or from an affected father. Each son born to a carrier mother has a 50% probability of inheriting the X chromosome carrying the mutant allele.
• Fragile X syndrome is a genetic condition involving changes in part of the X chromosome. It is the most common form of inherited intellectual disability (mental retardation) in males. It is caused by a change in a gene called FMR1. A small part of the gene code is repeated on a fragile area of the X chromosome. The more repeats, the more likely there is to be a problem. Males and females can both be affected, but because males have only one X chromosome, a single fragile X is likely to affect them more. Most fragile-X males have large testes, big ears, narrow faces, and sensory processing disorders that result in learning disabilities.

Other complications include:

• 46,XX testicular disorder of sex development, also called XX male syndrome, is a condition in which individuals with two X chromosomes in each cell, the pattern normally found in females, have a male appearance. People with this disorder have male external genitalia. In most people with 46,XX testicular disorder of sex development, the condition results from an exchange of genetic material between chromosomes (translocation). This exchange occurs as a random event during the formation of sperm cells in the affected person's father. The SRY gene (normally on the Y chromosome) is misplaced in this disorder, onto an X chromosome. Any person with an X chromosome that carries the SRY gene will develop male characteristics despite not having a Y chromosome.

Weathering

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Weathering 

 

A natural arch produced by erosion of differentially weathered rock in Jebel Kharaz (Jordan)

Weathering is the deterioration of rocks, soils and minerals as well as wood and artificial materials through contact with water, atmospheric gases, and biological organisms. Weathering occurs in situ (on site, with little or no movement), and so is distinct from erosion, which involves the transport of rocks and minerals by agents such as water, ice, snow, wind, waves and gravity.

Weathering processes are divided into physical and chemical weathering. Physical weathering involves the breakdown of rocks and soils through the mechanical effects of heat, water, ice, or other agents. Chemical weathering involves the chemical reaction of water, atmospheric gases, and biologically produced chemicals with rocks and soils. Water is the principal agent behind both physical and chemical weathering, though atmospheric oxygen and carbon dioxide and the activities of biological organisms are also important. Chemical weathering by biological action is also known as biological weathering.

The materials left over after the rock breaks down combine with organic material to create soil. Many of Earth's landforms and landscapes are the result of weathering processes combined with erosion and re-deposition. Weathering is a crucial part of the rock cycle, and sedimentary rock, formed from the weathering products of older rock, covers 66% of the Earth's continents and much of its ocean floor.

Physical weathering

Physical weathering, also called mechanical weathering or disaggregation, is the class of processes that causes the disintegration of rocks without chemical change.Physical weathering involves the breakdown of rocks into smaller fragments through processes such as expansion and contraction, mainly due to temperature changes. Two types of physical breakdown are freeze-thaw weathering and thermal fracturing. Pressure release can also cause weathering without temperature change. It is usually much less important than chemical weathering, but can be significant in subarctic or alpine environments. Furthermore, chemical and physical weathering often go hand in hand. For example, cracks extended by physical weathering will increase the surface area exposed to chemical action, thus amplifying the rate of disintegration.

Frost weathering is the most important form of physical weathering. Next in importance is wedging by plant roots, which sometimes enter cracks in rocks and pry them apart. The burrowing of worms or other animals may also help disintegrate rock, as can "plucking" by lichens.

Frost weathering

A rock in Abisko, Sweden fractured along existing joints possibly by frost weathering or thermal stress

 

Main article: Frost weathering

Frost weathering is the collective name for those forms of physical weathering that are caused by the formation of ice within rock outcrops. It was long believed that the most important of these is frost wedging, which results from the expansion of pore water when it freezes. However, a growing body of theoretical and experimental work suggests that ice segregation, in which supercooled water migrates to lenses of ice forming within the rock, is the more important mechanism.

When water freezes, its volume increases by 9.2%. This expansion can theoretically generate pressures greater that 200 megapascals (29,000 psi), though a more realistic upper limit is 14 megapascals (2,000 psi). This is still much greater than the tensile strength of granite, which is about 4 megapascals (580 psi). This makes frost wedging, in which pore water freezes and its volumetric expansion fractures the enclosing rock, appear to be a plausible mechanism for frost weathering. However, ice will simply expand out of a straight, open fracture before it can generate significant pressure. Thus frost wedging can only take place in small, tortuous fractures. The rock must also be almost completely saturated with water, or the ice will simply expand into the air spaces in the unsaturated rock without generating much pressure. These conditions are unusual enough that frost wedging is unlikely to be the dominant process of frost weathering. Frost wedging is most effective where there are daily cycles of melting and freezing of water-saturated rock, so it is unlikely to be significant in the tropics, in polar regions, or in arid climates.

Ice segregation is a less well characterized mechanism of physical weathering. It takes place because ice grains always have a surface layer, often just a few molecules thick, that resembles liquid water more than solid ice, even at temperatures well below the freezing point. This premelted liquid layer has unusual properties, including a strong tendency to draw in water by capillary action from warmer parts of the rock. This results in growth of the ice grain that puts considerable pressure on the surrounding rock, up to ten times greater than is likely with frost wedging. This mechanism is most effective in rock whose temperature averages just below the freezing point, −4 to −15 °C (25 to 5 °F). Ice segregation results in growth of ice needles and ice lenses within fractures in the rock, and parallel to the rock surface, that gradually pry the rock apart.

Thermal stress

Thermal stress weathering results from the expansion and contraction of rock due to temperature changes. Thermal stress weathering is most effective when the heated portion of the rock is buttressed by surrounding rock, so that it is free to expand in only one direction.

Thermal stress weathering comprises two main types, thermal shock and thermal fatigue. Thermal shock takes place when the stresses are so great that the rock cracks immediately, but this is uncommon. More typical is thermal fatigue, in which the stresses are not great enough to cause immediate rock failure, but repeated cycles of stress and release gradually weaken the rock.

Thermal stress weathering is an important mechanism in deserts, where there is a large diurnal temperature range, hot in the day and cold at night. As a result, thermal stress weathering is sometimes called insolation weathering, but this is misleading. Thermal stress weathering can be caused by any large change of temperature, and not just intense solar heating. It is likely as important in cold climates as in hot, arid climates. Wildfires can also be a significant cause of rapid thermal stress weathering.

The importance of thermal stress weathering has long been discounted by geologists, based on experiments in the early 20th century that seemed to show that its effects were unimportant. These experiments have since been criticized as unrealistic, since the rock samples were small, were polished (which reduces nucleation of fractures), and were not buttressed. These small samples were thus able to expand freely in all directions when heated in experimental ovens, which failed to produce the kinds of stress likely in natural settings. The experiments were also more sensitive to thermal shock than thermal fatigue, but thermal fatigue is likely the more important mechanism in nature. Geomorphologists have begun to reemphasize the importance of thermal stress weathering, particularly in cold climates.

Pressure release

See also: Erosion and tectonics

 

Exfoliated granite sheets in Texas, possibly caused by pressure release

Pressure release or unloading is a form of physical weathering seen when deeply buried rock is exhumed. Intrusive igneous rocks, such as granite, are formed deep beneath the Earth's surface. They are under tremendous pressure because of the overlying rock material. When erosion removes the overlying rock material, these intrusive rocks are exposed and the pressure on them is released. The outer parts of the rocks then tend to expand. The expansion sets up stresses which cause fractures parallel to the rock surface to form. Over time, sheets of rock break away from the exposed rocks along the fractures, a process known as exfoliation. Exfoliation due to pressure release is also known as sheeting.

As with thermal weathering, pressure release is most effective in buttressed rock. Here the differential stress directed towards the unbuttressed surface can be as high as 35 megapascals (5,100 psi), easily enough to shatter rock. This mechanism is also responsible for spalling in mines and quarries, and for the formation of joints in rock outcrops.

Retreat of an overlying glacier can also lead to exfoliation due to pressure release. This can be enhanced by other physical wearing mechanisms.

Salt-crystal growth

Tafoni at Salt Point State Park, Sonoma County, California

 

Main article: Haloclasty

Salt crystallization (also known as salt weathering, salt wedging or haloclasty) causes disintegration of rocks when saline solutions seep into cracks and joints in the rocks and evaporate, leaving salt crystals behind. As with ice segregation, the surfaces of the salt grains draw in additional dissolved salts through capillary action, causing the growth of salt lenses that exert high pressure on the surrounding rock. Sodium and magnesium salts are the most effective at producing salt weathering. Salt weathering can also take place when pyrite in sedimentary rock is chemically weathered to iron(II) sulfate and gypsum, which then crystallize as salt lenses.

Salt crystallization can take place wherever salts are concentrated by evaporation. It is thus most common in arid climates where strong heating causes strong evaporation and along coasts. Salt weathering is likely important in the formation of tafoni, a class of cavernous rock weathering structures.

Biological effects on mechanical weathering

Living organisms may contribute to mechanical weathering, as well as chemical weathering (see § Biological weathering below). Lichens and mosses grow on essentially bare rock surfaces and create a more humid chemical microenvironment. The attachment of these organisms to the rock surface enhances physical as well as chemical breakdown of the surface microlayer of the rock. Lichens have been observed to pry mineral grains loose from bare shale with their hyphae (rootlike attachment structures), a process described as plucking, and to pull the fragments into their body, where the fragments then undergo a process of chemical weathering not unlike digestion. On a larger scale, seedlings sprouting in a crevice and plant roots exert physical pressure as well as providing a pathway for water and chemical infiltration.

Chemical weathering

Comparison of unweathered (left) and weathered (right) limestone

Most rock forms at elevated temperature and pressure, and the minerals making up the rock are often chemically unstable in the relatively cool, wet, and oxidizing conditions typical of the Earth's surface. Chemical weathering takes place when water, oxygen, carbon dioxide, and other chemical substances react with rock to change its composition. These reactions convert some of the original primary minerals in the rock to secondary minerals, remove other substances as solutes, and leave the most stable minerals as a chemically unchanged resistate. In effect, chemical weathering changes the original set of minerals in the rock into a new set of minerals that is in closer equilibrium with surface conditions. However, true equilibrium is rarely reached, because weathering is a slow process, and leaching carries away solutes produced by weathering reactions before they can accumulate to equilibrium levels. This is particularly true in tropical environments.

Water is the principal agent of chemical weathering, converting many primary minerals to clay minerals or hydrated oxides via reactions collectively described as hydrolysis. Oxygen is also important, acting to oxidize many minerals, as is carbon dioxide, whose weathering reactions are described as carbonation.

The process of mountain block uplift is important in exposing new rock strata to the atmosphere and moisture, enabling important chemical weathering to occur; significant release occurs of Ca²⁺ and other ions into surface waters.

Dissolution

Limestone core samples at different stages of chemical weathering, from very high at shallow depths (bottom) to very low at greater depths (top). Slightly weathered limestone shows brownish stains, while highly weathered limestone loses much of its carbonate mineral content, leaving behind clay. Limestone drill core taken from the carbonate West Congolian deposit in Kimpese, Democratic Republic of Congo.

Dissolution (also called simple solution or congruent dissolution) is the process in which a mineral dissolves completely without producing any new solid substance. Rainwater easily dissolves soluble minerals, such as halite or gypsum, but can also dissolve highly resistant minerals such as quartz, given sufficient time. Water breaks the bonds between atoms in the crystal:

The overall reaction for dissolution of quartz is

SiO₂ + 2H₂O → H₄SiO₄

The dissolved quartz takes the form of silicic acid.

A particularly important form of dissolution is carbonate dissolution, in which atmospheric carbon dioxide enhances solution weathering. Carbonate dissolution affects rocks containing calcium carbonate, such as limestone and chalk. It takes place when rainwater combines with carbon dioxide to form carbonic acid, a weak acid, which dissolves calcium carbonate (limestone) and forms soluble calcium bicarbonate. Despite a slower reaction kinetics, this process is thermodynamically favored at low temperature, because colder water holds more dissolved carbon dioxide gas (due to the retrograde solubility of gases). Carbonate dissolution is therefore an important feature of glacial weathering.

Carbonate dissolution involves the following steps:

CO₂ + H₂O → H₂CO₃

carbon dioxide + water → carbonic acid

H₂CO₃ + CaCO₃ → Ca(HCO₃)₂

carbonic acid + calcium carbonate → calcium bicarbonate

Carbonate dissolution on the surface of well-jointed limestone produces a dissected limestone pavement. This process is most effective along the joints, widening and deepening them.

In unpolluted environments, the pH of rainwater due to dissolved carbon dioxide is around 5.6. Acid rain occurs when gases such as sulfur dioxide and nitrogen oxides are present in the atmosphere. These oxides react in the rain water to produce stronger acids and can lower the pH to 4.5 or even 3.0. Sulfur dioxide, SO₂, comes from volcanic eruptions or from fossil fuels, can become sulfuric acid within rainwater, which can cause solution weathering to the rocks on which it falls.

Hydrolysis and carbonation

Olivine weathering to iddingsite within a mantle xenolith

Hydrolysis (also called incongruent dissolution) is a form of chemical weathering in which only part of a mineral is taken into solution. The rest of the mineral is transformed into a new solid material, such as a clay mineral. For example, forsterite (magnesium olivine) is hydrolyzed into solid brucite and dissolved silicic acid:

Mg₂SiO₄ + 4 H₂O ⇌ 2 Mg(OH)₂ + H₄SiO₄

forsterite + water ⇌ brucite + silicic acid

Most hydrolysis during weathering of minerals is acid hydrolysis, in which protons (hydrogen ions), which are present in acidic water, attack chemical bonds in mineral crystals. The bonds between different cations and oxygen ions in minerals differ in strength, and the weakest will be attacked first. The result is that minerals in igneous rock weather in roughly the same order in which they were originally formed (Bowen's Reaction Series). Relative bond strength is shown in the following table:

Bond	Relative strength
Si–O	2.4
Ti–O	1.8
Al–O	1.65
Fe+3–O	1.4
Mg–O	0.9
Fe+2–O	0.85
Mn–O	0.8
Ca–O	0.7
Na–O	0.35
K–O	0.25

This table is only a rough guide to order of weathering. Some minerals, such as illite, are unusually stable, while silica is unusually unstable given the strength of the silicon-oxygen bond.

Carbon dioxide that dissolves in water to form carbonic acid is the most important source of protons, but organic acids are also important natural sources of acidity. Acid hydrolysis from dissolved carbon dioxide is sometimes described as carbonation, and can result in weathering of the primary minerals to secondary carbonate minerals. For example, weathering of forsterite can produce magnesite instead of brucite via the reaction:

Mg₂SiO₄ + 2 CO₂ + 2 H₂O ⇌ 2 MgCO₃ + H₄SiO₄

forsterite + carbon dioxide + water ⇌ magnesite + silicic acid in solution

Carbonic acid is consumed by silicate weathering, resulting in more alkaline solutions because of the bicarbonate. This is an important reaction in controlling the amount of CO₂ in the atmosphere and can affect climate.

Aluminosilicates containing highly soluble cations, such as sodium or potassium ions, will release the cations as dissolved bicarbonates during acid hydrolysis:

2 KAlSi₃O₈ + 2 H₂CO₃ + 9 H₂O ⇌ Al₂Si₂O₅(OH)₄ + 4 H₄SiO₄ + 2 K⁺ + 2 HCO₃⁻

orthoclase (aluminosilicate feldspar) + carbonic acid + water ⇌ kaolinite (a clay mineral) + silicic acid in solution + potassium and bicarbonate ions in solution

Oxidation

A pyrite cube has dissolved away from host rock, leaving gold particles behind.

 

Oxidized pyrite cubes

Within the weathering environment, chemical oxidation of a variety of metals occurs. The most commonly observed is the oxidation of Fe²⁺ (iron) by oxygen and water to form Fe³⁺ oxides and hydroxides such as goethite, limonite, and hematite. This gives the affected rocks a reddish-brown coloration on the surface which crumbles easily and weakens the rock. Many other metallic ores and minerals oxidize and hydrate to produce colored deposits, as does sulfur during the weathering of sulfide minerals such as chalcopyrites or CuFeS₂ oxidizing to copper hydroxide and iron oxides.

Hydration

Mineral hydration is a form of chemical weathering that involves the rigid attachment of water molecules or H+ and OH- ions to the atoms and molecules of a mineral. No significant dissolution takes place. For example, iron oxides are converted to iron hydroxides and the hydration of anhydrite forms gypsum.

Bulk hydration of minerals is secondary in importance to dissolution, hydrolysis, and oxidation, but hydration of the crystal surface is the crucial first step in hydrolysis. A fresh surface of a mineral crystal exposes ions whose electrical charge attracts water molecules. Some of these molecules break into H+ that bonds to exposed anions (usually oxygen) and OH- that bonds to exposed cations. This further disrupts the surface, making it susceptible to various hydrolysis reactions. Additional protons replace cations exposed in the surface, freeing the cations as solutes. As cations are removed, silicon-oxygen and silicon-aluminium bonds become more susceptible to hydrolysis, freeing silicic acid and aluminium hydroxides to be leached away or to form clay minerals. Laboratory experiments show that weathering of feldspar crystals begins at dislocations or other defects on the surface of the crystal, and that the weathering layer is only a few atoms thick. Diffusion within the mineral grain does not appear to be significant.

A freshly broken rock shows differential chemical weathering (probably mostly oxidation) progressing inward. This piece of sandstone was found in glacial drift near Angelica, New York.

Biological weathering

Mineral weathering can also be initiated or accelerated by soil microorganisms. Soil organisms make up about 10 mg/cm³ of typical soils, and laboratory experiments have demonstrated that albite and muscovite weather twice as fast in live versus sterile soil. Lichens on rocks are among the most effective biological agents of chemical weathering. For example, an experimental study on hornblende granite in New Jersey, USA, demonstrated a 3x – 4x increase in weathering rate under lichen covered surfaces compared to recently exposed bare rock surfaces.

Biological weathering of basalt by lichen, La Palma

The most common forms of biological weathering result from the release of chelating compounds (such as certain organic acids and siderophores) and of carbon dioxide and organic acids by plants. Roots can build up the carbon dioxide level to 30% of all soil gases, aided by adsorption of CO₂ on clay minerals and the very slow diffusion rate of CO₂ out of the soil. The CO₂ and organic acids help break down aluminium- and iron-containing compounds in the soils beneath them. Roots have a negative electrical charge balanced by protons in the soil next to the roots, and these can be exchanged for essential nutrient cations such as potassium. Decaying remains of dead plants in soil may form organic acids which, when dissolved in water, cause chemical weathering. Chelating compounds, mostly low molecular weight organic acids, are capable of removing metal ions from bare rock surfaces, with aluminium and silicon being particularly susceptible. The ability to break down bare rock allows lichens to be among the first colonizers of dry land. The accumulation of chelating compounds can easily affect surrounding rocks and soils, and may lead to podsolisation of soils.

The symbiotic mycorrhizal fungi associated with tree root systems can release inorganic nutrients from minerals such as apatite or biotite and transfer these nutrients to the trees, thus contributing to tree nutrition. It was also recently evidenced that bacterial communities can impact mineral stability leading to the release of inorganic nutrients. A large range of bacterial strains or communities from diverse genera have been reported to be able to colonize mineral surfaces or to weather minerals, and for some of them a plant growth promoting effect has been demonstrated. The demonstrated or hypothesised mechanisms used by bacteria to weather minerals include several oxidoreduction and dissolution reactions as well as the production of weathering agents, such as protons, organic acids and chelating molecules.

Weathering on the ocean floor

Weathering of basaltic oceanic crust differs in important respects from weathering in the atmosphere. Weathering is relatively slow, with basalt becoming less dense, at a rate of about 15% per 100 million years. The basalt becomes hydrated, and is enriched in total and ferric iron, magnesium, and sodium at the expense of silica, titanium, aluminum, ferrous iron, and calcium.

Building weathering

Concrete damaged by acid rain

Buildings made of any stone, brick or concrete are susceptible to the same weathering agents as any exposed rock surface. Also statues, monuments and ornamental stonework can be badly damaged by natural weathering processes. This is accelerated in areas severely affected by acid rain.

Accelerated building weathering may be a threat to the environment and occupant safety. Design strategies can moderate the impact of environmental effects, such as using of pressure-moderated rain screening, ensuring that the HVAC system is able to effectively control humidity accumulation and selecting concrete mixes with reduced water content to minimize the impact of freeze-thaw cycles. 

Properties of well-weathered soils

Granitic rock, which is the most abundant crystalline rock exposed at the Earth's surface, begins weathering with destruction of hornblende. Biotite then weathers to vermiculite, and finally oligoclase and microcline are destroyed. All are converted into a mixture of clay minerals and iron oxides. The resulting soil is depleted in calcium, sodium, and ferrous iron compared with the bedrock, and magnesium is reduced 40% and silicon by 15%. At the same time, the soil is enriched in aluminium and potassium, by at least 50%; by titanium, whose abundance triples; and by ferric iron, whose abundance increases by an order of magnitude compared with the bedrock.

Basaltic rock is more easily weathered than granitic rock, due to its formation at higher temperatures and drier conditions. The fine grain size and presence of volcanic glass also hasten weathering. In tropical settings, it rapidly weathers to clay minerals, aluminium hydroxides, and titanium-enriched iron oxides. Because most basalt is relatively poor in potassium, the basalt weathers directly to potassium-poor montmorillonite, then to kaolinite. Where leaching is continuous and intense, as in rain forests, the final weathering product is bauxite, the principal ore of aluminium. Where rainfall is intense but seasonal, as in monsoon climates, the final weathering product is iron- and titanium-rich laterite.  Conversion of kaolinite to bauxite occurs only with intense leaching, as ordinary river water is in equilibrium with kaolinite.

Soil formation requires between 100 and 1,000 years, a very brief interval in geologic time. As a result, some formations show numerous paleosol (fossil soil) beds. For example, the Willwood Formation of Wyoming contains over 1,000 paleosol layers in a 770 meters (2,530 ft) section representing 3.5 million years of geologic time. Paleosols have been identified in formations as old as Archean (over 2.5 billion years in age). However, paleosols are difficult to recognize in the geologic record. Indications that a sedimentary bed is a paleosol include a gradational lower boundary and sharp upper boundary, the presence of much clay, poor sorting with few sedimentary structures, rip-up clasts in overlying beds, and desiccation cracks containing material from higher beds.

The degree of weathering of a soil can be expressed as the chemical index of alteration, defined as 100 Al₂O₃/(Al₂O₃ + CaO + Na₂O + K₂O). This varies from 47 for unweathered upper crust rock to 100 for fully weathered material.

Weathering of non-geological materials

Wood can be physically and chemically weathered by hydrolysis and other processes relevant to minerals, but in addition, wood is highly susceptible to weathering induced by ultraviolet radiation from sunlight. This induces photochemical reactions that degrade the wood surface. Photochemical reactions are also significant in the weathering of paint and plastics.

Gallery

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  Salt weathering of building stone on the island of Gozo, Malta

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  Salt weathering of sandstone near Qobustan, Azerbaijan

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  Permian sandstone wall near Sedona, Arizona, United States, weathered into a small alcove

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  Weathering on a sandstone pillar in Bayreuth

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  Weathering effect of acid rain on statues

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  Weathering effect on a sandstone statue in Dresden, Germany

Conjugated system

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Conjugated_system 

 

Cinnamaldehyde is a naturally-occurring compound that has a conjugated system

 

penta-1,3-diene is a molecule with a conjugated system

 

Diazomethane conjugated pi-system

In chemistry, a conjugated system is a system of connected p orbitals with delocalized electrons in a molecule, which in general lowers the overall energy of the molecule and increases stability. It is conventionally represented as having alternating single and multiple bonds. Lone pairs, radicals or carbenium ions may be part of the system, which may be cyclic, acyclic, linear or mixed. The term "conjugated" was coined in 1899 by the German chemist Johannes Thiele.

Conjugation is the overlap of one p orbital with another across an adjacent σ bond (in transition metals d orbitals can be involved).

A conjugated system has a region of overlapping p orbitals, bridging the interjacent locations that simple diagrams illustrate as not having a π bond. They allow a delocalization of π electrons across all the adjacent aligned p orbitals. The π electrons do not belong to a single bond or atom, but rather to a group of atoms.

Molecules containing conjugated systems of orbitals and electrons are called conjugated molecules, which have overlapping p orbitals on three or more atoms. Some simple organic conjugated molecules are 1,3-butadiene, benzene, and allylic carbocations. The largest conjugated systems are found in graphene, graphite, conductive polymers and carbon nanotubes.

Chemical bonding in conjugated systems

Some prototypical examples of species with delocalized bonding. Top row: pyridine, furan, tropylium cation. Second row: allyl radical, acetate ion, acrolein. Atoms involved are in bold red, while electrons involved in delocalized bonding are in blue. (Particular attention should be paid to the involvement or non-involvement of "non-bonding" electrons.)

Conjugation is possible by means of alternating single and double bonds in which each atom supplies a p orbital perpendicular to the plane of the molecule. However, that is not the only way for conjugation to take place. As long as each contiguous atom in a chain has an available p orbital, the system can be considered conjugated. For example, furan is a five-membered ring with two alternating double bonds flanking an oxygen. The oxygen has two lone pairs, one of which occupies a p orbital perpendicular to the ring on that position, thereby maintaining the conjugation of that five-membered ring by overlap with the perpendicular p orbital on each of the adjacent carbon atoms. The other lone pair remains in plane and does not participate in conjugation.

In general, any sp² or sp-hybridized carbon or heteroatom, including ones bearing an empty orbital or lone pair orbital, can participate in conjugated systems, though lone pairs do not always participate in a conjugated system. For example, in pyridine, the nitrogen atom already participates in the conjugated system through a formal double bond with an adjacent carbon, so the lone pair remains in the plane of the ring in an sp² hybrid orbital and does not participate in the conjugation. A requirement for conjugation is orbital overlap; thus, the conjugated system must be planar (or nearly so). As a consequence, lone pairs which do participate in conjugated systems will occupy orbitals of pure p character instead of spⁿ hybrid orbitals typical for nonconjugated lone pairs.

The π system of furan and lone pairs. Note that one of the oxygen lone pairs participates in conjugation in a p orbital, while the other lone pair is in an sp² hybridized orbital in the plane of the molecule and not part of the π system. The participation of six electrons in the π system makes furan aromatic (see below).

A common model for the treatment of conjugated molecules is a composite valence bond / Hückel molecular orbital theory (VB/HMOT) treatment, in which the σ framework of the molecule is separated from the π system (or systems) of the molecule (see the article on the sigma-pi and equivalent-orbital models for this model and an alternative treatment). Although σ bonding can be treated using a delocalized approach as well, it is generally the π bonding that is being considered when delocalized bonding is invoked in the context of simple organic molecules.

Sigma (σ) framework: The σ framework is described by a strictly localized bonding scheme and consists of σ bonds formed from the interactions between sp³-, sp²-, and sp-hybridized atomic orbitals on the main group elements (and 1s atomic orbitals on hydrogen), together with localized lone pairs derived from filled, nonbonding hybrid orbitals. The interaction that results in σ bonding takes the form of head-to-head overlap of the larger lobe of each hybrid orbital (or the single spherical lobe of a hydrogen 1s orbital). Each atomic orbital contributes one electron when the orbitals overlap pairwise to form two-electron σ bonds, or two electrons when the orbital constitutes a lone pair. These localized orbitals (bonding and non-bonding) are all located in the plane of the molecule, with σ bonds mainly localized between nuclei along the internuclear axis.

Pi (π) system or systems: Orthogonal to the σ framework described above, π bonding occurs above and below the plane of the molecule where σ bonding takes place. The π system(s) of the molecule are formed by the interaction of unhybridized p atomic orbitals on atoms employing sp²- and sp-hybridization. The interaction that results in π bonding takes place between p orbitals that are adjacent by virtue of a σ bond joining the atoms and takes the form of side-to-side overlap of the two equally large lobes that make up each p orbital. Atoms that are sp³-hybridized do not have an unhybridized p orbital available for participation in π bonding and their presence necessarily terminates a π system or separates two π systems. A basis p orbital that takes part in a π system can contribute one electron (which corresponds to half of a formal "double bond"), two electrons (which corresponds to a delocalized "lone pair"), or zero electrons (which corresponds to a formally "empty" orbital). Bonding for π systems formed from the overlap of more than two p orbitals is handled using the Hückel approach to obtain a zeroth order (qualitative) approximation of the π symmetry molecular orbitals that result from delocalized π bonding.

Using the σ/π-separation scheme to describe bonding, the Lewis resonance structures of a molecule like diazomethane can be translated into a bonding picture consisting of π-systems and localized lone pairs superimposed on a localized framework of σ-bonds.

This simple model for chemical bonding is successful for the description of most normal-valence molecules consisting of only s- and p-block elements, although systems that involve electron-deficient bonding, including nonclassical carbocations, lithium and boron clusters, and hypervalent centers require significant modifications in which σ bonds are also allowed to delocalize and are perhaps better treated with canonical molecular orbitals that are delocalized over the entire molecule. Likewise, d- and f-block organometallics are also inadequately described by this simple model. Bonds in strained small rings (such as cyclopropane or epoxide) are not well-described by strict σ/π separation, as bonding between atoms in the ring consists of "bent bonds" or "banana bonds" that are bowed outward and are intermediate in nature between σ and π bonds. Nevertheless, organic chemists frequently use the language of this model to rationalize the structure and reactivity of typical organic compounds.

Electrons in conjugated π systems are shared by all adjacent sp²- and sp-hybridized atoms that contribute overlapping, parallel p atomic orbitals. As such, the atoms and π-electrons involved behave as one large bonded system. These systems are often referred to 'n-center k-electron π-bonds,' compactly denoted by the symbol Π^k
_n, to emphasize this behavior. For example, the delocalized π electrons in acetate anion and benzene are said to be involved in Π⁴
₃ and Π⁶
₆ systems, respectively (see the article on three-center four-electron bonding). It is important to recognize that, generally speaking, these multi-center bonds correspond to the occupation of several molecular orbitals (MOs) with varying degrees of bonding or non-bonding character (filling of orbitals with antibonding character is uncommon). Each one is occupied by one or two electrons in accordance with the aufbau principle and Hund's rule. Cartoons showing overlapping p orbitals, like the one for benzene below, show the basis p atomic orbitals before they are combined to form molecular orbitals. In compliance with the Pauli exclusion principle, overlapping p orbitals do not result in the formation of one large MO containing more than two electrons.

Hückel MO theory is commonly used approach to obtain a zeroth order picture of delocalized π molecular orbitals, including the mathematical sign of the wavefunction at various parts of the molecule and the locations of nodal planes. It is particularly easy to apply for conjugated hydrocarbons and provides a reasonable approximation as long as the molecule is assumed to be planar with good overlap of p orbitals.

Stabilization energy

The quantitative estimation of stabilization from conjugation is notoriously contentious and depends on the implicit assumptions that are made when comparing reference systems or reactions. The energy of stabilization is known as the resonance energy when formally defined as the difference in energy between the real chemical species and the hypothetical species featuring localized π bonding that corresponds to the most stable resonance form. This energy cannot be measured, and a precise definition accepted by most chemists will probably remain elusive. Nevertheless, some broad statements can be made. In general, stabilization is more significant for cationic systems than neutral ones. For buta-1,3-diene, a crude measure of stabilization is the activation energy for rotation of the C2-C3 bond. This places the resonance stabilization at around 6 kcal/mol. Comparison of heats of hydrogenation of 1,4-pentadiene and 1,3-pentadiene estimates a slightly more modest value of 3.5 kcal/mol. For comparison, allyl cation has a gas-phase rotation barrier of around 38 kcal/mol, a much greater penalty for loss of conjugation. Comparison of hydride ion affinities of propyl cation and allyl cation, corrected for inductive effects, results in a considerably lower estimate of the resonance energy at 20–22 kcal/mol. Nevertheless, it is clear that conjugation stabilizes allyl cation to a much greater extent than buta-1,3-diene. In contrast to the usually minor effect of neutral conjugation, aromatic stabilization can be considerable. Estimates for the resonance energy of benzene range from around 36–73 kcal/mol.

Generalizations and related concepts

Homoconjugation weakens the double bond character of the C=O bond, resulting in a lower IR frequency.

There are also other types of interactions that generalize the idea of interacting p orbitals in a conjugated system. The concept of hyperconjugation holds that certain σ bonds can also delocalize into a low-lying unoccupied orbital of a π system or an unoccupied p orbital. Hyperconjugation is commonly invoked to explain the stability of alkyl substituted radicals and carbocations. Hyperconjugation is less important for species in which all atoms satisfy the octet rule, but a recent computational study supports hyperconjugation as the origin of the increased stability of alkenes with a higher degree of substitution (Zaitsev's rule).

Homoconjugation is an overlap of two π-systems separated by a non-conjugating group, such as CH₂. Unambiguous examples are comparatively rare in neutral systems, due to a comparatively minor energetic benefit that is easily overridden by a variety of other factors; however, they are common in cationic systems in which a large energetic benefit can be derived from delocalization of positive charge (see the article on homoaromaticity for details.). Neutral systems generally require constrained geometries favoring interaction to produce significant degrees of homoconjugation. In the example below, the carbonyl stretching frequencies of the IR spectra of the respective compounds demonstrate homoconjugation, or lack thereof, in the neutral ground state molecules.

Due to the partial π character of formally σ bonds in a cyclopropane ring, evidence for transmission of "conjugation" through cyclopropanes has also been obtained.

Two appropriately aligned π systems whose ends meet at right angles can engage in spiroconjugation.

Conjugated cyclic compounds

Basis p orbitals of benzene.

 

Benzene π molecular orbitals according to Hückel theory. Molecular orbitals are frequently described as linear combinations of atomic orbitals, whose coefficients are indicated here by the size and shading of the orbital lobes.

Cyclic compounds can be partly or completely conjugated. Annulenes, completely conjugated monocyclic hydrocarbons, may be aromatic, nonaromatic or antiaromatic.

Aromatic compounds

Compounds that have a monocyclic, planar conjugated system containing (4n + 2) π-electrons for whole numbers n are aromatic and exhibit an unusual stability. The classic example benzene has a system of six π electrons, which, together with the planar ring of C–C σ bonds containing 12 electrons and radial C–H σ bonds containing six electrons, forms the thermodynamically and kinetically stable benzene ring, the common core of the benzenoid aromatic compounds. For benzene itself, there are two equivalent conjugated contributing Lewis structures (the so-called Kekulé structures) that predominate. The true electronic structure is therefore a quantum-mechanical combination (resonance hybrid) of these contributors, which results in the experimentally observed C–C bonds which are intermediate between single and double bonds and of equal strength and length. In the molecular orbital picture, the six p atomic orbitals of benzene combine to give six molecular orbitals. Three of these orbitals, which lie at lower energies than the isolated p orbital and are therefore net bonding in character (one molecular orbital is strongly bonding, while the other two are equal in energy but bonding to a lesser extent) are occupied by six electrons, while three destabilized orbitals of overall antibonding character remain unoccupied. The result is strong thermodynamic and kinetic aromatic stabilization. Both models describe rings of π electron density above and below the framework of C–C σ bonds.

Nonaromatic and antiaromatic compounds

Cyclooctatetraene. Adjacent double bonds are not coplanar. The double bonds are therefore not conjugated.

Not all compounds with alternating double and single bonds are aromatic. Cyclooctatetraene, for example, possesses alternating single and double bonds. The molecule typically adopts a "tub" conformation. Because the p orbitals of the molecule do not align themselves well in this non-planar molecule, the π bonds are essentially isolated and not conjugated. The lack of conjugation allows the 8 π electron molecule to avoid antiaromaticity, a destabilizing effect associated with cyclic, conjugated systems containing 4n π (n = 0, 1, 2, ...) electrons. This effect is due to the placement of two electrons into two degenerate nonbonding (or nearly nonbonding) orbitals of the molecule, which, in addition to drastically reducing the thermodynamic stabilization of delocalization, would either force the molecule to take on triplet diradical character, or cause it to undergo Jahn-Teller distortion to relieve the degeneracy. This has the effect of greatly increasing the kinetic reactivity of the molecule. Because of the lack of long-range interactions, cyclooctatetraene takes on a nonplanar conformation and is nonaromatic in character, behaving as a typical alkene. In contrast, derivatives of the cyclooctatetraene dication and dianion have been found to be planar experimentally, in accord with the prediction that they are stabilized aromatic systems with 6 and 10 π electrons, respectively. Because antiaromaticity is a property that molecules try to avoid whenever possible, only a few experimentally observed species are believed to be antiaromatic. Cyclobutadiene and cyclopentadienyl cation are commonly cited as examples of antiaromatic systems.

In pigments

In a conjugated pi-system, electrons are able to capture certain photons as the electrons resonate along a certain distance of p-orbitals - similar to how a radio antenna detects photons along its length. Typically, the more conjugated (longer) the pi-system is, the longer the wavelength of photon can be captured. Compounds whose molecules contain a sufficient number of conjugated bonds can absorb light in the visible region, and therefore appear colorful to the eye, usually appearing yellow or red.

Many dyes make use of conjugated electron systems to absorb visible light, giving rise to strong colors. For example, the long conjugated hydrocarbon chain in beta-carotene leads to its strong orange color. When an electron in the system absorbs a photon of light of the right wavelength, it can be promoted to a higher energy level. A simple model of the energy levels is provided by the quantum-mechanical problem of a one-dimensional particle in a box of length L, representing the movement of a π electron along a long conjugated chain of carbon atoms. In this model the lowest possible absorption energy corresponds to the energy difference between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO). For a chain of n C=C bonds or 2n carbon atoms in the molecular ground state, there are 2n π electrons occupying n molecular orbitals, so that the energy gap is

${\displaystyle E_{n+1}-E_{n}={\frac {(2n+1)\hbar ^{2}\pi ^{2}}{2mL^{2}}}}$

Since the box length L increases approximately linearly with the number of C=C bonds n, this means that the energy ΔE of a photon absorbed in the HOMO–LUMO transition is approximately proportional to 1/n. The photon wavelength λ = hc/ΔE is then approximately proportional to n. Although this model is very approximate, λ does in general increase with n (or L) for similar molecules. For example, the HOMO–LUMO absorption wavelengths for conjugated butadiene, hexatriene and octatetraene are 217 nm, 252 nm and 304 nm respectively. However, for good numerical agreement of the particle in a box model with experiment, the single-bond/double-bond bond length alternations of the polyenes must be taken into account. Alternatively, one can use the Hückel method which is also designed to model the electronic structure of conjugated systems.

Many electronic transitions in conjugated π-systems are from a predominantly bonding molecular orbital (MO) to a predominantly antibonding MO (π to π^*), but electrons from non-bonding lone pairs can also be promoted to a π-system MO (n to π^*) as often happens in charge-transfer complexes. A HOMO to LUMO transition is made by an electron if it is allowed by the selection rules for electromagnetic transitions. Conjugated systems of fewer than eight conjugated double bonds absorb only in the ultraviolet region and are colorless to the human eye. With every double bond added, the system absorbs photons of longer wavelength (and lower energy), and the compound ranges from yellow to red in color. Compounds that are blue or green typically do not rely on conjugated double bonds alone.

This absorption of light in the ultraviolet to visible spectrum can be quantified using ultraviolet–visible spectroscopy, and forms the basis for the entire field of photochemistry.

Conjugated systems that are widely used for synthetic pigments and dyes are diazo and azo compounds and phthalocyanine compounds.

Phthalocyanine compounds

Conjugated systems not only have low energy excitations in the visible spectral region but they also accept or donate electrons easily. Phthalocyanines, which, like Phthalocyanine Blue BN and Phthalocyanine Green G, often contain a transition metal ion, exchange an electron with the complexed transition metal ion that easily changes its oxidation state. Pigments and dyes like these are charge-transfer complexes.

Copper phthalocyanine

Porphyrins and similar compounds

Porphyrins have conjugated molecular ring systems (macrocycles) that appear in many enzymes of biological systems. As a ligand, porphyrin forms numerous complexes with metallic ions like iron in hemoglobin that colors blood red. Hemoglobin transports oxygen to the cells of our bodies. Porphyrin–metal complexes often have strong colors. A similar molecular structural ring unit called chlorin is similarly complexed with magnesium instead of iron when forming part of the most common forms of chlorophyll molecules, giving them a green color. Another similar macrocycle unit is corrin, which complexes with cobalt when forming part of cobalamin molecules, constituting Vitamin B12, which is intensely red. The corrin unit has six conjugated double bonds but is not conjugated all the way around its macrocycle ring.

Heme group of hemoglobin	The chlorin section of the chlorophyll a molecule. The green box shows a group that varies between chlorophyll types.	Cobalamin structure includes a corrin macrocycle.

Chromophores

Conjugated systems form the basis of chromophores, which are light-absorbing parts of a molecule that can cause a compound to be colored. Such chromophores are often present in various organic compounds and sometimes present in polymers that are colored or glow in the dark. Chromophores often consist of a series of conjugated bonds and/or ring systems, commonly aromatic, which can include C–C, C=C, C=O, or N=N bonds.

Chemical structure of beta-carotene. The eleven conjugated double bonds that form the chromophore of the molecule are highlighted in red.

Conjugated chromophores are found in many organic compounds including azo dyes (also artificial food additives), compounds in fruits and vegetables (lycopene and anthocyanidins), photoreceptors of the eye, and some pharmaceutical compounds such as the following:

This polyene antimycotic called Amphotericin B has a conjugated system with seven double bonds acting as a chromophore that absorbs strongly in the ultraviolet–visible spectrum, giving it a yellow color.