Industrial fermentation

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

Industrial fermentation is the intentional use of fermentation in manufacturing processes. In addition to the mass production of fermented foods and drinks, industrial fermentation has widespread applications in chemical industry. Commodity chemicals, such as acetic acid, citric acid, and ethanol are made by fermentation. Moreover, nearly all commercially produced industrial enzymes, such as lipase, invertase and rennet, are made by fermentation with genetically modified microbes. In some cases, production of biomass itself is the objective, as is the case for single-cell proteins, baker's yeast, and starter cultures for lactic acid bacteria used in cheesemaking.

In general, fermentations can be divided into four types:

• Production of biomass (viable cellular material)
• Production of extracellular metabolites (chemical compounds)
• Production of intracellular components (enzymes and other proteins)
• Transformation of substrate (in which the transformed substrate is itself the product)

These types are not necessarily disjoined from each other, but provide a framework for understanding the differences in approach. The organisms used are typically microorganisms, particularly bacteria, algae, and fungi, such as yeasts and molds, but industrial fermentation may also involve cell cultures from plants and animals, such as CHO cells and insect cells. Special considerations are required for the specific organisms used in the fermentation, such as the dissolved oxygen level, nutrient levels, and temperature. The rate of fermentation depends on the concentration of microorganisms, cells, cellular components, and enzymes as well as temperature, pH and level of oxygen for aerobic fermentation. Product recovery frequently involves the concentration of the dilute solution.

General process overview

In most industrial fermentations, the organisms or eukaryotic cells are submerged in a liquid medium; in others, such as the fermentation of cocoa beans, coffee cherries, and miso, fermentation takes place on the moist surface of the medium.

There are also industrial considerations related to the fermentation process. For instance, to avoid biological process contamination, the fermentation medium, air, and equipment are sterilized. Foam control can be achieved by either mechanical foam destruction or chemical anti-foaming agents. Several other factors must be measured and controlled such as pressure, temperature, agitator shaft power, and viscosity. An important element for industrial fermentations is scale up. This is the conversion of a laboratory procedure to an industrial process. It is well established in the field of industrial microbiology that what works well at the laboratory scale may work poorly or not at all when first attempted at large scale. It is generally not possible to take fermentation conditions that have worked in the laboratory and blindly apply them to industrial scale equipment. Although many parameters have been tested for use as scale up criteria, there is no general formula because of the variation in fermentation processes. The most important methods are the maintenance of constant power consumption per unit of broth and the maintenance of constant volumetric transfer rate.

Phases of growth

Bacterial growth curve

Fermentation begins once the growth medium is inoculated with the organism of interest. Growth of the inoculum does not occur immediately. This is the period of adaptation, called the lag phase. Following the lag phase, the rate of growth of the organism steadily increases, for a certain period—this period is the log or exponential phase.

After a phase of exponential growth, the rate of growth slows down, due to the continuously falling concentrations of nutrients and/or a continuously increasing (accumulating) concentrations of toxic substances. This phase, where the increase of the rate of growth is checked, is the deceleration phase. After the deceleration phase, growth ceases and the culture enters a stationary phase or a steady state. The biomass remains constant, except when certain accumulated chemicals in the culture chemically break down the cells in a process called chemolysis. Unless other microorganisms contaminate the culture, the chemical constitution remains unchanged. If all of the nutrients in the medium are consumed, or if the concentration of toxins is too great, the cells may become senescent and begin to die off. The total amount of biomass may not decrease, but the number of viable organisms will decrease.

Fermentation medium

The microbes or eukaryotic cells used for fermentation grow in (or on) specially designed growth medium which supplies the nutrients required by the organisms or cells. A variety of media exist, but invariably contain a carbon source, a nitrogen source, water, salts, and micronutrients. In the production of wine, the medium is grape must. In the production of bio-ethanol, the medium may consist mostly of whatever inexpensive carbon source is available.

Carbon sources are typically sugars or other carbohydrates, although in the case of substrate transformations (such as the production of vinegar) the carbon source may be an alcohol or something else altogether. For large scale fermentations, such as those used for the production of ethanol, inexpensive sources of carbohydrates, such as molasses, corn steep liquor, sugar cane juice, or sugar beet juice are used to minimize costs. More sensitive fermentations may instead use purified glucose, sucrose, glycerol or other sugars, which reduces variation and helps ensure the purity of the final product. Organisms meant to produce enzymes such as beta galactosidase, invertase or other amylases may be fed starch to select for organisms that express the enzymes in large quantity.

Fixed nitrogen sources are required for most organisms to synthesize proteins, nucleic acids and other cellular components. Depending on the enzyme capabilities of the organism, nitrogen may be provided as bulk protein, such as soy meal; as pre-digested polypeptides, such as peptone or tryptone; or as ammonia or nitrate salts. Cost is also an important factor in the choice of a nitrogen source. Phosphorus is needed for production of phospholipids in cellular membranes and for the production of nucleic acids. The amount of phosphate which must be added depends upon the composition of the broth and the needs of the organism, as well as the objective of the fermentation. For instance, some cultures will not produce secondary metabolites in the presence of phosphate.

Growth factors and trace nutrients are included in the fermentation broth for organisms incapable of producing all of the vitamins they require. Yeast extract is a common source of micronutrients and vitamins for fermentation media. Inorganic nutrients, including trace elements such as iron, zinc, copper, manganese, molybdenum, and cobalt are typically present in unrefined carbon and nitrogen sources, but may have to be added when purified carbon and nitrogen sources are used. Fermentations which produce large amounts of gas (or which require the addition of gas) will tend to form a layer of foam, since fermentation broth typically contains a variety of foam-reinforcing proteins, peptides or starches. To prevent this foam from occurring or accumulating, antifoaming agents may be added. Mineral buffering salts, such as carbonates and phosphates, may be used to stabilize pH near optimum. When metal ions are present in high concentrations, use of a chelating agent may be necessary.

Developing an optimal medium for fermentation is a key concept in efficient optimization. One-factor-at-a-time (OFAT) is the preferential choice that researchers use for designing a medium composition. This method involves changing only one factor at a time while keeping the other concentrations constant. This method can be separated into some sub groups. One is Removal Experiments. In this experiment all the components of the medium are removed one at a time and their effects on the medium are observed. Supplementation experiments involve evaluating the effects of nitrogen and carbon supplements on production. The final experiment is a replacement experiment. This involves replacing the nitrogen and carbon sources that show an enhancement effect on the intended production. Overall OFAT is a major advantage over other optimization methods because of its simplicity.

Production of biomass

Microbial cells or biomass is sometimes the intended product of fermentation. Examples include single cell protein, bakers yeast, lactobacillus, E. coli, and others. In the case of single-cell protein, algae is grown in large open ponds which allow photosynthesis to occur. If the biomass is to be used for inoculation of other fermentations, care must be taken to prevent mutations from occurring.

Production of extracellular metabolites

Metabolites can be divided into two groups: those produced during the growth phase of the organism, called primary metabolites and those produced during the stationary phase, called secondary metabolites. Some examples of primary metabolites are ethanol, citric acid, glutamic acid, lysine, vitamins and polysaccharides. Some examples of secondary metabolites are penicillin, cyclosporin A, gibberellin, and lovastatin.

Primary metabolites

Primary metabolites are compounds made during the ordinary metabolism of the organism during the growth phase. A common example is ethanol or lactic acid, produced during glycolysis. Citric acid is produced by some strains of Aspergillus niger as part of the citric acid cycle to acidify their environment and prevent competitors from taking over. Glutamate is produced by some Micrococcus species, and some Corynebacterium species produce lysine, threonine, tryptophan and other amino acids. All of these compounds are produced during the normal "business" of the cell and released into the environment. There is therefore no need to rupture the cells for product recovery.

Secondary metabolites

Secondary metabolites are compounds made in the stationary phase; penicillin, for instance, prevents the growth of bacteria which could compete with Penicillium molds for resources. Some bacteria, such as Lactobacillus species, are able to produce bacteriocins which prevent the growth of bacterial competitors as well. These compounds are of obvious value to humans wishing to prevent the growth of bacteria, either as antibiotics or as antiseptics (such as gramicidin S). Fungicides, such as griseofulvin are also produced as secondary metabolites. Typically secondary metabolites are not produced in the presence of glucose or other carbon sources which would encourage growth, and like primary metabolites are released into the surrounding medium without rupture of the cell membrane.

In the early days of the biotechnology industry, most biopharmaceutical products were made in E. coli; by 2004 more biopharmaceuticals were manufactured in eukaryotic cells, such as CHO cells, than in microbes, but used similar bioreactor systems. Insect cell culture systems came into use in the 2000s as well.

Production of intracellular components

Of primary interest among the intracellular components are microbial enzymes: catalase, amylase, protease, pectinase, cellulase, hemicellulase, lipase, lactase, streptokinase and many others. Recombinant proteins, such as insulin, hepatitis B vaccine, interferon, granulocyte colony-stimulating factor, streptokinase and others are also made this way. The largest difference between this process and the others is that the cells must be ruptured (lysed) at the end of fermentation, and the environment must be manipulated to maximize the amount of the product. Furthermore, the product (typically a protein) must be separated from all of the other cellular proteins in the lysate to be purified.

Transformation of substrate

Substrate transformation involves the transformation of a specific compound into another, such as in the case of phenylacetylcarbinol, and steroid biotransformation, or the transformation of a raw material into a finished product, in the case of food fermentations and sewage treatment.

Food fermentation

Main article: Fermentation in food processing

In the history of food, ancient fermented food processes, such as making bread, wine, cheese, curds, idli, dosa, among others can be dated to more than seven thousand years ago. They were developed long before humanity had any knowledge of the existence of the microorganisms involved. Some foods such as Marmite are the byproduct of the fermentation process, in this case in the production of beer.

Ethanol fuel

Fermentation is the main source of ethanol in the production of ethanol fuel. Common crops such as sugar cane, potato, cassava, and maize are fermented by yeast to produce ethanol which is further processed to become fuel.

Sewage treatment

In the process of sewage treatment, sewage is digested by enzymes secreted by bacteria. Solid organic matters are broken down into harmless, soluble substances and carbon dioxide. Liquids that result are disinfected to remove pathogens before being discharged into rivers or the sea or can be used as liquid fertilizers. Digested solids, known also as sludge, is dried and used as fertilizer. Gaseous byproducts such as methane can be utilized as biogas to fuel electrical generators. One advantage of bacterial digestion is that it reduces the bulk and odor of sewage, thus reducing space needed for dumping. The main disadvantage of bacterial digestion in sewage disposal is that it is a very slow process.

Agricultural feed

A wide variety of agroindustrial waste products can be fermented to use as food for animals, especially ruminants. Fungi have been employed to break down cellulosic wastes to increase protein content and improve in vitro digestibility.

Precision fermentation

Precision fermentation is an approach to manufacturing specific functional products which intends to minimise the production of unwanted by-products through the application of synthetic biology, particularly by generating synthetic "cell factories" with engineered genomes and metabolic pathways optimised to produce the desired compounds as efficiently as possible with the available resources. Precision fermentation of genetically modified microorganisms may be used to manufacture proteins needed for cell culture media, providing for serum-free cell culture media in the manufacturing process of cultured meat. A 2021 publication showed that photovoltaic-driven microbial protein production could use 10 times less land for an equivalent amount of protein compared to soybean cultivation. Some Food Regulatory Agencies such as the FDA do not require the labeling of precision fermented foods as GMO since they are produced by, but do not contain the genetically engineered organisms. It is unclear how regulation will be handled in EU markets, with some Startups such as Formo and Those Vegan Cowboys forming the Food Fermentation Europe (FFE) alliance together with other alt-protein startups to seek regulatory approval.

Organic superconductor

From Wikipedia, the free encyclopedia

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

An organic superconductor is a synthetic organic compound that exhibits superconductivity at low temperatures.

As of 2007 the highest achieved critical temperature for an organic superconductor at standard pressure is 33 K (−240 °C; −400 °F), observed in the alkali-doped fullerene RbCs₂C₆₀.

In 1979 Klaus Bechgaard synthesized the first organic superconductor (TMTSF)₂PF₆ (the corresponding material class was named after him later) with a transition temperature of T_C = 0.9 K (−272.2 °C; −458.0 °F), at an external pressure of 12,000 bar (170,000 psi).

Many materials may be characterized as organic superconductors. These include the Bechgaard salts and Fabre salts which are both quasi-one-dimensional, and quasi-two-dimensional materials such as k-BEDT-TTF₂X charge-transfer complex, λ-BETS₂X compounds, graphite intercalation compounds and three-dimensional materials such as the alkali-doped fullerenes.

Organic superconductors are of special interest not only for scientists, looking for room-temperature superconductivity and for model systems explaining the origin of superconductivity but also for daily life issues as organic compounds are mainly built of carbon and hydrogen which belong to the most common elements on earth in contrast to copper or osmium.

One-dimensional Fabre and Bechgaard salts

Fabre-salts are composed of tetramethyltetrathiafulvalene (TMTTF) and Bechgaard salts of tetramethyltetraselenafulvalene (TMTSF). These two organic molecules are similar except for the sulfur-atoms of TMTTF being replaced by selenium-atoms in TMTSF. The molecules are stacked in columns (with a tendency to dimerization) which are separated by anions. Typical anions are, for example, octahedral PF₆, AsF₆ or tetrahedral ClO₄ or ReO₄.

Both material classes are quasi-one-dimensional at room-temperature, only conducting along the molecule stacks, and share a very rich phase diagram containing antiferromagnetic ordering, charge order, spin-density wave state, dimensional crossover and superconductivity.

Only one Bechgaard salt was found to be superconducting at ambient pressure which is (TMTTF)₂ClO₄ with a transition temperature of T_C = 1.4 K (−271.8 °C; −457.1 °F). Several other salts become superconducting only under external pressure. The external pressure required to drive most Fabre-salts to superconductivity is so high, that under lab conditions superconductivity was observed only in one compound. A selection of the transition temperature and corresponding external pressure of several one-dimensional organic superconductors is shown in the table below.

Material	TC (K)	pext (kbar)
(TMTSF)2SbF6	0.36	10.5
(TMTSF)2PF6	1.1	6.5
(TMTSF)2AsF6	1.1	9.5
(TMTSF)2ReO4	1.2	9.5
(TMTSF)2TaF6	1.35	11
(TMTTF)2Br	0.8	26

Two-dimensional (BEDT-TTF)₂X

The layered structure of ET₂X salts illustrated by κ-(ET)₂Cu₂(CN)₃. The yellow, grey, blue and red ellipsoids represent the sulfur, carbon, nitrogen and copper atoms, respectively. The hydrogen atoms are omitted for clarity. Layers of ET donor molecules are separated by polymeric Cu₂(CN)₃⁻ anion sheets. κ-(ET)₂Cu₂(CN)₃ is a semiconductor, but a very similar κ'-(ET)₂Cu₂(CN)₃ polymorph is an ambient-pressure superconductor with T_C ~ 5 K.

BEDT-TTF is the short form of bisethylenedithio-tetrathiafulvalene commonly abbreviated with ET. These molecules form planes which are separated by anions. The pattern of the molecules in the planes is not unique but there are several different phases growing, depending on the anion and the growth conditions. Important phases concerning superconductivity are the α- and θ- phase with the molecules ordering in a fishbone structure and the β- and especially κ-phase which order in a checkerboard structure with molecules being dimerized in the κ-phase. This dimerization makes the κ-phases special as they are not quarter- but half-filled systems, driving them into superconductivity at higher temperatures compared to the other phases.

The amount of possible anions separating two sheets of ET-molecules is nearly infinite. There are simple anions such as triiodide (I⁻
₃), polymeric ones such as the very famous Cu[N(CN)₂]Br and anions containing solvents for example Ag(CF₃)₄·112DCBE. The electronic properties of the ET-based crystals are determined by its growing phase, its anion and by the external pressure applied. The external pressure needed to drive an ET-salt with insulating ground state to a superconducting one is much less than those needed for Bechgaard salts. For example, κ-(ET)₂Cu[N(CN)₂]Cl needs only a pressure of about 300 bar (4,400 psi) to become superconducting, which can be achieved by placing a crystal in grease frozen below 0 °C (32 °F) and then providing sufficient stress to induce the superconducting transition. The crystals are very sensitive, which can be observed impressively in α-(ET)₂I₃ lying several hours in the sun (or more controlled in an oven at 40 °C, 104 °F). After this treatment one gets α_Tempered-(ET)₂I₃ which is superconducting.

In contrast to the Fabre or Bechgaard salts universal phase diagrams for all the ET-based salts have only been proposed yet. Such a phase diagram would depend not only on temperature and pressure (i.e. bandwidth), but also on electronic correlations. In addition to the superconducting ground state these materials show charge-order, antiferromagnetism or remain metallic down to lowest temperatures. One compound is even predicted to be a spin liquid.

The highest transition temperatures at ambient pressure and with external pressure are both found in κ-phases with very similar anions. κ-(ET)₂Cu[N(CN)₂]Br becomes superconducting at T_C = 11.8 K (−261.3 °C; −438.4 °F) at ambient pressure, and a pressure of 300 bar drives deuterated κ-(ET)₂Cu[N(CN)₂]Cl from an antiferromagnetic to a superconducting ground state with a transition temperature of T_C = 13.1 K (−260.0 °C; −436.1 °F). The following table shows only a few exemplary superconductors of this class. For more superconductors, see Lebed (2008) in the references.

Material	TC (K)	pext (kbar)
βH-(ET)2I3	1.5	0
θ-(ET)2I3	3.6	0
k-(ET)2I3	3.6	0
α-(ET)2KHg(SCN)4	0.3	0
α-(ET)2KHg(SCN)4	1.2	1.2
β’’-(ET)2SF5CH2CF2SO3	5.3	0
κ-(ET)2Cu[N(CN)2]Cl	12.8	0.3
κ-(ET)2Cu[N(CN)2]Cl deuterated	13.1	0.3
κ-(ET)2Cu[N(CN)2]Br deuterated	11.2	0
κ-(ET)2Cu(NCS)2	10.4	0
κ-(ET)4Hg2.89Cl8	1.8	12
κH-(ET)2Cu(CF3)4·TCE	9.2	0
κH-(ET)2Ag(CF3)4·TCE	11.1	0

Even more superconductors can be found by changing the ET-molecules slightly either by replacing the sulfur atoms by selenium (BEDT-TSF, BETS) or by oxygen (BEDO-TTF, BEDO).

Some two-dimensional organic superconductors of the κ-(ET)₂X and λ(BETS)₂X families are candidates for the Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) phase when superconductivity is suppressed by an external magnetic field.

Doped fullerenes

Structure of Cs₃C₆₀

Superconducting fullerenes based on C₆₀ are fairly different from other organic superconductors. The building molecules are no longer manipulated hydrocarbons but pure carbon molecules. In addition these molecules are no longer flat but bulky which gives rise to a three-dimensional, isotropic superconductor. The pure C₆₀ grows in an fcc-lattice and is an insulator. By placing alkali atoms in the interstitials the crystal becomes metallic and eventually superconducting at low temperatures.

Unfortunately C₆₀ crystals are not stable at ambient atmosphere. They are grown and investigated in closed capsules, limiting the measurement techniques possible. The highest transition temperature measured so far was T_C = 33 K (−240.2 °C; −400.3 °F) for Cs₂RbC₆₀.The highest measured transition temperature of an organic superconductor was found in 1995 in Cs₃C₆₀ pressurized with 15,000 bar (220,000 psi) to be T_C = 40 K (−233.2 °C; −387.7 °F). Under pressure this compound shows a unique behavior. Usually the highest T_C is achieved with the lowest pressure necessary to drive the transition. Further increase of the pressure usually reduces the transition temperature. However, in Cs₃C₆₀ superconductivity sets in at very low pressures of several 100 bar, and the transition temperature keeps increasing with increasing pressure. This indicates a completely different mechanism than just broadening of the bandwidth.

Material	TC (K)	pext (mbar)
K3C60	18	0
Rb3C60	30.7	0
K2CsC60	24	0
K2RbC60	21.5	0
K5C60	8.4	0
Sr6C60	6.8	0
(NH3)4Na2CsC60	29.6	0
(NH3)K3C60	28	14.8

More organic superconductors

Next to the three major classes of organic superconductors (SCs) there are more organic systems becoming superconducting at low temperatures or under pressure. A few examples follow.

TTP-based SCs

TMTTF as well as BEDT-TTF are based on the molecule TTF (tetrathiafulvalene). Using tetrathiapentalene (TTP) as basic molecules one receives a variety of new organic molecules serving as cations in organic crystals. Some of them are superconducting. This class of superconductors was only reported recently and investigations are still under process.

Phenanthrene-type SCs

Instead of using sulfated molecules or the fairly big Buckminster fullerenes recently it became possible to synthesize crystals from the hydrocarbon picene and phenanthrene. Doping the crystal picene and phenanthrene with alkali metals such as potassium or rubidium and annealing for several days leads to superconductivity with transition temperatures up to 18 K (−255 °C; −427 °F). For AxPhenanthrene, the superconductivity is possible unconventional. Both phenanthrene and picene are called phenanthrene-edge-type polycyclic aromatic hydrocarbon. The increasing number of benzene rings results in higher T_c.

Graphite intercalation SCs

Crystal structure of KC₈

Putting foreign molecules or atoms between hexagon graphite sheets leads to ordered structures and to superconductivity even if neither the foreign molecule or atom nor the graphite layers are metallic. Several stoichiometries have been synthesized using mainly alkali atoms as anions.

Several T_Cs for unusual SCs

Material	TC (K)
(BDA-TTP)2AsF6	5.8
(DTEDT)3Au(CN)2	4
K3.3Picene	18
Rb3.1Picene	6.9
K3Phenanthrene	4.95
Rb3Phenanthrene	4.75
CaC5	11.5
NaC2	5
KC8	0.14

Charge-transfer complex

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https://en.wikipedia.org/wiki/Charge-transfer_complex 

Structure of one part of one stack of the charge-transfer complex between pyrene and 1,3,5-trinitrobenzene.

In chemistry, charge-transfer (CT) complex, or electron donor-acceptor complex, describes a type of supramolecular assembly of two or more molecules or ions. The assembly consists of two molecules that self-attract through electrostatic forces, i.e., one has at least partial negative charge and the partner has partial positive charge, referred to respectively as the electron acceptor and electron donor. In some cases, the degree of charge transfer is "complete", such that the CT complex can be classified as a salt. In other cases, the charge-transfer association is weak, and the interaction can be disrupted easily by polar solvents.

Examples

Electron donor-acceptor complexes

A number of organic compounds form charge-transfer complex, which are often described as electron-donor-acceptor complexes (EDA complexes). Typical acceptors are nitrobenzenes or tetracyanoethylene (TCNE). The strength of their interaction with electron donors correlates with the ionization potentials of the components. For TCNE, the stability constants (L/mol) for its complexes with benzene derivatives correlates with the number of methyl groups: benzene (0.128), 1,3,5-trimethylbenzene (1.11), 1,2,4,5-tetramethylbenzene (3.4), and hexamethylbenzene (16.8). A simple example for a prototypical electron-donor-acceptor complexes is nitroaniline.

1,3,5-Trinitrobenzene and related polynitrated aromatic compounds, being electron-deficient, form charge-transfer complexes with many arenes. Such complexes form upon crystallization, but often dissociate in solution to the components. Characteristically, these CT salts crystallize in stacks of alternating donor and acceptor (nitro aromatic) molecules, i.e. A-B-A-B.

Dihalogen/interhalogen CT complexes

Early studies on donor-acceptor complexes focused on the solvatochromism exhibited by iodine, which often results from I₂ forming adducts with electron donors such as amines and ethers. Dihalogens X₂ (X = Cl, Br, I) and interhalogens XY(X = I; Y = Cl, Br) are Lewis acid species capable of forming a variety of products when reacted with donor species. Among these species (including oxidation or protonated products), CT adducts D·XY have been largely investigated. The CT interaction has been quantified and is the basis of many schemes for parameterizing donor and acceptor properties, such as those devised by Gutmann, Childs, Beckett, and the ECW model.

Many organic species featuring chalcogen or pnictogen donor atoms form CT salts. The nature of the resulting adducts can be investigated both in solution and in the solid state.

In solution, the intensity of charge-transfer bands in the UV-Vis absorbance spectrum is strongly dependent upon the degree (equilibrium constant) of this association reaction. Methods have been developed to determine the equilibrium constant for these complexes in solution by measuring the intensity of absorption bands as a function of the concentration of donor and acceptor components in solution. The Benesi-Hildebrand method, named for its developers, was first described for the association of iodine dissolved in aromatic hydrocarbons.

In the solid state a valuable parameter is the elongation of the X–X or X–Y bond length, resulting from the antibonding nature of the σ* LUMO. The elongation can be evaluated by means of structural determinations (XRD)^[10] and FT-Raman spectroscopy.

A well-known example is the complex formed by iodine when combined with starch, which exhibits an intense purple charge-transfer band. This has widespread use as a rough screen for counterfeit currency. Unlike most paper, the paper used in US currency is not sized with starch. Thus, formation of this purple color on application of an iodine solution indicates a counterfeit.

TTF-TCNQ: prototype for electrically conducting complexes

Edge-on view of portion of crystal structure of hexamethyleneTTF/TCNQ charge transfer salt, highlighting the segregated stacking.

End-on view of portion of crystal structure of hexamethyleneTTF/TCNQ charge transfer salt. The distance between the TTF planes is 3.55 Å.

In 1954, charge-transfer salts derived from perylene with iodine or bromine were reported with resistivities as low as 8 ohm·cm. In 1973, it was discovered that a combination of tetracyanoquinodimethane (TCNQ) and tetrathiafulvalene (TTF) forms a strong charge-transfer complex referred to as TTF-TCNQ. The solid shows almost metallic electrical conductance and was the first-discovered purely organic conductor. In a TTF-TCNQ crystal, TTF and TCNQ molecules are arranged independently in separate parallel-aligned stacks, and an electron transfer occurs from donor (TTF) to acceptor (TCNQ) stacks. Hence, electrons and electron holes are separated and concentrated in the stacks and can traverse in a one-dimensional direction along the TCNQ and TTF columns, respectively, when an electric potential is applied to the ends of a crystal in the stack direction.

Superconductivity is exhibited by tetramethyl-tetraselenafulvalene-hexafluorophosphate (TMTSF₂PF₆), which is a semi-conductor at ambient conditions, shows superconductivity at low temperature (critical temperature) and high pressure: 0.9 K and 12 kbar. Critical current densities in these complexes are very small.

Mechanistic implications

Many reactions involving nucleophiles attacking electrophiles can be usefully assessed from the perspective of an incipient charge-transfer complex. Examples include electrophilic aromatic substitution, the addition of Grignard reagents to ketones, and brominolysis of metal-alkyl bonds.

Electronic structure

The electronic structure of a charge-transfer (CT) complex is a result of the electronic coupling between an electron donor (D) and an electron acceptor (A), in which partial or complete redistribution of electronic charge can take place. Unlike isolated molecules, CT complexes are typically characterized by electronic wavefunctions that are mixtures of neutral and ionic structures rather than those of individual molecules. The electronic ground and excited states of a CT complex may be characterized via two limiting diabatic structures: a neutral one, ${\displaystyle |D^0{A}^0⟩}$, and an ionic one, ${\displaystyle |D^{+}{A}^{-}⟩}$, associated with electron transfer between the donor and acceptor. The actual electronic ground and excited states are linear combinations of these structures. Observable effects including the permanent dipole moment, optical absorption intensity, and degree of charge separation are thus dependent on the contribution of the ionic part to these states.

A traditional theoretical representation of the CT complex can be described via a two-state Hamiltonian, expressed in the basis of neutral and ionic diabatic configurations, ${\displaystyle \hat{H}=\left(\begin{array}{cc}{E}_N& V_{DA}\\ V_{DA}& E_I\end{array}\right)}$

where ${\displaystyle E_N}$ and ${\displaystyle E_I}$ are the diabatic energies of the neutral and ionic states, respectively, and ${\displaystyle V_{DA}}$ indicates the donor–acceptor electronic coupling. The diagonalized form of this Hamiltonian gives adiabatic electronic states, whose energies and charge-transfer character depend on both the energy separation of the diabatic states and the strength of the donor–acceptor coupling.

A molecular orbital description of charge transfer is usually used, in which the donor and acceptor frontier molecular orbitals dominate the interaction. The HOMO of the donor and the LUMO of the acceptor generally govern the CT interaction. Optical excitation corresponding to a CT transition can be considered as promotion of an electron from the donor HOMO to the acceptor LUMO, resulting in increased electronic charge separation and a large transition dipole moment.

The energy difference between neutral and ionic diabatic structures is governed by key electronic parameters including the donor ionization potential, acceptor electron affinity, and the Coulomb interaction between the resultant charges. Together, these quantities dictate the thermodynamic driving force for charge transfer and the resulting equilibrium degree of ionicity of the CT complex.

Charge-transfer absorption bands arise from electronic transitions between mixed neutral and ionic states and are distinct from local excitations of the individual donor or acceptor molecules. These CT absorption bands are determined by both the diabatic energy splitting and the electronic coupling strength, and are typically analyzed using the Mulliken–Hush approach.

The environment of CT complexes has a strong influence on their electronic structure. Increased solvation stabilizes the ionic configuration relative to the neutral state and often enhances charge separation, shifting CT absorption bands to lower energies. Differences in donor–acceptor distance and mutual orientation similarly influence the electronic coupling and the observed magnitude of charge transfer.

Electron transport chain

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

An electron transport chain (ETC) is a series of protein complexes and other molecules which transfer electrons from electron donors to electron acceptors via redox reactions (both reduction and oxidation occurring simultaneously) and couples this electron transfer with the transfer of protons (H⁺ ions) across a membrane. Many of the enzymes in the electron transport chain are embedded within the membrane.

The flow of electrons through the electron transport chain is an exergonic process. The energy from the redox reactions creates an electrochemical proton gradient that drives the synthesis of adenosine triphosphate (ATP). In aerobic respiration, the flow of electrons terminates with molecular oxygen as the final electron acceptor. In anaerobic respiration, other electron acceptors are used, such as sulfate.

In an electron transport chain, the redox reactions are driven by the difference in the Gibbs free energy of reactants and products. The free energy released when a higher-energy electron donor and acceptor convert to lower-energy products, while electrons are transferred from a lower to a higher redox potential, is used by the complexes in the electron transport chain to create an electrochemical gradient of ions. It is this electrochemical gradient that drives the synthesis of ATP via coupling with oxidative phosphorylation through ATP synthase.

In eukaryotic organisms, the electron transport chain, and site of oxidative phosphorylation, is found on the inner mitochondrial membrane. The energy released by reactions of oxygen and reduced compounds such as cytochrome c and (indirectly) NADH and FADH₂ is used by the electron transport chain to pump protons into the intermembrane space, generating the electrochemical gradient over the inner mitochondrial membrane. In photosynthetic eukaryotes, the electron transport chain is found on the thylakoid membrane. Here, light energy drives electron transport through a proton pump and the resulting proton gradient causes subsequent synthesis of ATP. In bacteria, the electron transport chain can vary between species but it always constitutes a set of redox reactions that are coupled to the synthesis of ATP through the generation of an electrochemical gradient and oxidative phosphorylation through ATP synthase.

Mitochondrial electron transport chains

The electron transport chain in the mitochondrion is the site of oxidative phosphorylation in eukaryotes. It mediates the reaction between NADH or succinate generated in the citric acid cycle and oxygen to power ATP synthase.

Most eukaryotic cells have mitochondria, which produce ATP from reactions of oxygen with products of the citric acid cycle, fatty acid metabolism, and amino acid metabolism. At the inner mitochondrial membrane, electrons from NADH and FADH₂ pass through the electron transport chain to oxygen, which provides the energy driving the process as it is reduced to water. The electron transport chain comprises an enzymatic series of electron donors and acceptors. Each electron donor will pass electrons to an acceptor of higher redox potential, which in turn donates these electrons to another acceptor, a process that continues down the series until electrons are passed to oxygen, the terminal electron acceptor in the chain. Each reaction releases energy because a higher-energy donor and acceptor convert to lower-energy products. Via the transferred electrons, this energy is used to generate a proton gradient across the mitochondrial membrane by "pumping" protons into the intermembrane space, producing a state of higher free energy that has the potential to do work. This entire process is called oxidative phosphorylation since ADP is phosphorylated to ATP by using the electrochemical gradient that the redox reactions of the electron transport chain have established driven by energy-releasing reactions of oxygen.

Mitochondrial redox carriers

Energy associated with the transfer of electrons down the electron transport chain is used to pump protons from the mitochondrial matrix into the intermembrane space, creating an electrochemical proton gradient (ΔpH) across the inner mitochondrial membrane. This proton gradient is largely but not exclusively responsible for the mitochondrial membrane potential (ΔΨ_M). It allows ATP synthase to use the flow of H⁺ through the enzyme back into the matrix to generate ATP from adenosine diphosphate (ADP) and inorganic phosphate. Complex I (NADH coenzyme Q reductase; labeled I) accepts electrons from the Krebs cycle electron carrier nicotinamide adenine dinucleotide (NADH), and passes them to coenzyme Q (ubiquinone; labeled Q), which also receives electrons from Complex II (succinate dehydrogenase; labeled II). Q passes electrons to Complex III (cytochrome bc₁ complex; labeled III), which passes them to cytochrome c (cyt c). Cyt c passes electrons to Complex IV (cytochrome c oxidase; labeled IV).

Four membrane-bound complexes have been identified in mitochondria. Each is an extremely complex transmembrane structure that is embedded in the inner membrane. Three of them are proton pumps. The structures are electrically connected by lipid-soluble electron carriers and water-soluble electron carriers. The overall electron transport chain can be summarized as follows:

Complex I

Further information: Respiratory complex I

In Complex I (NADH ubiquinone oxidoreductase, Type I NADH dehydrogenase, or mitochondrial complex I; EC 7.1.1.2), two electrons are removed from NADH and transferred to a lipid-soluble carrier, ubiquinone (Q). The reduced product, ubiquinol (QH₂), freely diffuses within the membrane, and Complex I translocates four protons (H⁺) across the membrane, thus producing a proton gradient. Complex I is one of the main sites at which premature electron leakage to oxygen occurs, thus being one of the main sites of production of superoxide.

The pathway of electrons is as follows:

NADH is oxidized to NAD⁺, by reducing flavin mononucleotide to FMNH₂ in one two-electron step. FMNH₂ is then oxidized in two one-electron steps, through a semiquinone intermediate. Each electron thus transfers from the FMNH₂ to an Fe–S cluster, from the Fe-S cluster to ubiquinone (Q). Transfer of the first electron results in the free-radical (semiquinone) form of Q, and transfer of the second electron reduces the semiquinone form to the ubiquinol form, QH₂. During this process, four protons are translocated from the mitochondrial matrix to the intermembrane space. As the electrons move through the complex an electron current is produced along the 180 Angstrom width of the complex within the membrane. This current powers the active transport of four protons to the intermembrane space per two electrons from NADH.

Complex II

In Complex II (succinate dehydrogenase or succinate-CoQ reductase; EC 1.3.5.1) additional electrons are delivered into the quinone pool (Q) originating from succinate and transferred (via flavin adenine dinucleotide (FAD)) to Q. Complex II consists of four protein subunits: succinate dehydrogenase (SDHA); succinate dehydrogenase [ubiquinone] iron–sulfur subunit mitochondrial (SDHB); succinate dehydrogenase complex subunit C (SDHC); and succinate dehydrogenase complex subunit D (SDHD). Other electron donors (e.g., fatty acids and glycerol 3-phosphate) also direct electrons into Q (via FAD). Complex II is a parallel electron transport pathway to Complex I, but unlike Complex I, no protons are transported to the intermembrane space in this pathway. Therefore, the pathway through Complex II contributes less energy to the overall electron transport chain process.

Complex III

In Complex III (cytochrome bc₁ complex or CoQH₂-cytochrome c reductase; EC 7.1.1.8), the Q-cycle contributes to the proton gradient by an asymmetric absorption/release of protons. Two electrons are removed from QH₂ at the Q_O site and sequentially transferred to two molecules of cytochrome c, a water-soluble electron carrier located within the intermembrane space. The two other electrons sequentially pass across the protein to the Q_i site where the quinone part of ubiquinone is reduced to quinol. A proton gradient is formed by one quinol (${\displaystyle 2{\text{H}}_2^{+}{\text{e}}^{-}}$) oxidations at the Q_o site to form one quinone (${\displaystyle 2{\text{H}}_2^{+}{\text{e}}^{-}}$) at the Q_i site. (In total, four protons are translocated: two protons reduce quinone to quinol and two protons are released from two ubiquinol molecules.)

${\displaystyle {\text{QH}}_2^{}+2}$${\displaystyle \text{ cytochrome }c}$${\displaystyle ({\text{Fe}}^{\text{III}})+2\text{H}}$${\displaystyle {}_{\text{in}}^{+}}$${\displaystyle ⟶\text{Q}+2}$${\displaystyle \text{ cytochrome }c}$${\displaystyle ({\text{Fe}}^{\text{II}})+4\text{H}}$${\displaystyle {}_{\text{out}}^{+}}$

When electron transfer is reduced (by a high membrane potential or respiratory inhibitors such as antimycin A), Complex III may leak electrons to molecular oxygen, resulting in superoxide formation.

This complex is inhibited by dimercaprol (British Anti-Lewisite, BAL), naphthoquinone and antimycin.

Complex IV

In Complex IV (cytochrome c oxidase; EC 7.1.1.9), sometimes called cytochrome AA3, four electrons are removed from four molecules of cytochrome c and transferred to molecular oxygen (O₂) and four protons, producing two molecules of water. The complex contains coordinated copper ions and several heme groups. At the same time, eight protons are removed from the mitochondrial matrix (although only four are translocated across the membrane), contributing to the proton gradient. The exact details of proton pumping in Complex IV are still under study. Cyanide is an inhibitor of Complex IV.

Coupling with oxidative phosphorylation

Depiction of ATP synthase, the site of oxidative phosphorylation to generate ATP.

According to the chemiosmotic coupling hypothesis, proposed by Nobel Prize in Chemistry winner Peter D. Mitchell, the electron transport chain and oxidative phosphorylation are coupled by a proton gradient across the inner mitochondrial membrane. The efflux of protons from the mitochondrial matrix creates an electrochemical gradient (proton gradient). This gradient is used by the F_OF₁ ATP-synthase complex to make ATP via oxidative phosphorylation. ATP-synthase is sometimes described as Complex V of the electron transport chain.

The F_O component acts as a channel that harnesses the proton flow to drive rotation. It is composed of a, b and c subunits. Protons in the inter-membrane space of mitochondria first enter the ATP-synthase complex through an a subunit channel. Then protons bind to the c subunits, which are oriented in a ring (the c-ring), where the number of c subunits determines how many protons are required to make the c-ring and the attached γ-rotor turn one full revolution. There are 8 c subunits in humans, thus 8 protons are required. Protons are released as a result of the rotation of the c-ring, being directed into the mitochondrial matrix along the a subunit channels. This proton reflux drives the mechanical rotation of the c-ring and the γ-axle. The rotation of the γ-rotor causes the sequential alternation of conformational states in the catalytic β-subunits in F₁.

There are three different conformational states, which are:

• Open, in this state the β-subunit has low affinity to ligands, releasing the previously synthesized ATP molecule.
• Loose, Binds ADP and P_i together loosely.
• Tight, Binds ADP and P_i so tightly that it catalyzes the condensation reaction to form ATP.

This cycle is known as the binding change mechanism (coined by Paul D. Boyer), explaining the conversion of mechanical rotation to chemical energy.

Coupling with oxidative phosphorylation is a key step for ATP production. However, in specific cases, uncoupling the two processes may be biologically useful. The uncoupling protein, thermogenin—present in the inner mitochondrial membrane of brown adipose tissue—provides for an alternative flow of protons back to the inner mitochondrial matrix. Thyroxine is also a natural uncoupler. This alternative flow results in thermogenesis rather than ATP production.

Reverse electron flow

Reverse electron flow is the transfer of electrons through the electron transport chain through the reverse redox reactions. Usually requiring a significant amount of energy to be used, this can reduce the oxidized forms of electron donors. For example, NAD⁺ can be reduced to NADH by Complex I. There are several factors that have been shown to induce reverse electron flow. However, more work needs to be done to confirm this. One example is blockage of ATP synthase, resulting in a build-up of protons and therefore a higher proton-motive force, inducing reverse electron flow.

Prokaryotic electron transport chains

In eukaryotes, NADH is the most important electron donor. The associated electron transport chain is NADH → Complex I → Q → Complex III → cytochrome c → Complex IV → O₂ where Complexes I, III and IV are proton pumps, while Q and cytochrome c are mobile electron carriers. The electron acceptor for this process is molecular oxygen.

In prokaryotes (bacteria and archaea) the situation is more complicated, because there are several different electron donors and several different electron acceptors. The generalized electron transport chain in bacteria is:

Electrons can enter the chain at three levels: at the level of a dehydrogenase, at the level of the quinone pool, or at the level of a mobile cytochrome electron carrier. These levels correspond to successively more positive redox potentials, or to successively decreased potential differences relative to the terminal electron acceptor. In other words, they correspond to successively smaller Gibbs free energy changes for the overall redox reaction.

Individual bacteria use multiple electron transport chains, often simultaneously. Bacteria can use a number of different electron donors, a number of different dehydrogenases, a number of different oxidases and reductases, and a number of different electron acceptors. For example, E. coli (when growing aerobically using glucose and oxygen as an energy source) uses two different NADH dehydrogenases and two different quinol oxidases, for a total of four different electron transport chains operating simultaneously.

A common feature of all electron transport chains is the presence of a proton pump to create an electrochemical gradient over a membrane. Bacterial electron transport chains may contain as many as three proton pumps, like mitochondria, or they may contain two or at least one.

Electron donors

In the current biosphere, the most common electron donors are organic molecules. Organisms that use organic molecules as an electron source are called organotrophs. Chemoorganotrophs (animals, fungi, protists) and photolithotrophs (plants and algae) constitute the vast majority of all familiar life forms.

Some prokaryotes can use inorganic matter as an electron source. Such an organism is called a (chemo)lithotroph ("rock-eater"). Inorganic electron donors include hydrogen, carbon monoxide, ammonia, nitrite, sulfur, sulfide, manganese oxide, and ferrous iron. Lithotrophs have been found growing in rock formations thousands of meters below the surface of Earth. Because of their volume of distribution, lithotrophs may actually outnumber organotrophs and phototrophs in our biosphere.

The use of inorganic electron donors such as hydrogen as an energy source is of particular interest in the study of evolution. This type of metabolism must logically have preceded the use of organic molecules and oxygen as an energy source.

Dehydrogenases: equivalents to complexes I and II

Bacteria can use several different electron donors. When organic matter is the electron source, the donor may be NADH or succinate, in which case electrons enter the electron transport chain via NADH dehydrogenase (similar to Complex I in mitochondria) or succinate dehydrogenase (similar to Complex II). Other dehydrogenases may be used to process different energy sources: formate dehydrogenase, lactate dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, H₂ dehydrogenase (hydrogenase),electron transport chain. Some dehydrogenases are also proton pumps, while others funnel electrons into the quinone pool. Most dehydrogenases show induced expression in the bacterial cell in response to metabolic needs triggered by the environment in which the cells grow. In the case of lactate dehydrogenase in E. coli, the enzyme is used aerobically and in combination with other dehydrogenases. It is inducible and is expressed when the concentration of DL-lactate in the cell is high.

Quinone carriers

Quinones are mobile, lipid-soluble carriers that shuttle electrons (and protons) between large, relatively immobile macromolecular complexes embedded in the membrane. Bacteria use ubiquinone (Coenzyme Q, the same quinone that mitochondria use) and related quinones such as menaquinone (Vitamin K₂). Archaea in the genus Sulfolobus use caldariellaquinone. The use of different quinones is due to slight changes in redox potentials caused by changes in structure. The change in redox potentials of these quinones may be suited to changes in the electron acceptors or variations of redox potentials in bacterial complexes.

Proton pumps

A proton pump is any process that creates a proton gradient across a membrane. Protons can be physically moved across a membrane, as seen in mitochondrial Complexes I and IV. The same effect can be produced by moving electrons in the opposite direction. The result is the disappearance of a proton from the cytoplasm and the appearance of a proton in the periplasm. Mitochondrial Complex III is this second type of proton pump, which is mediated by a quinone (the Q cycle).

Some dehydrogenases are proton pumps, while others are not. Most oxidases and reductases are proton pumps, but some are not. Cytochrome bc₁ is a proton pump found in many, but not all, bacteria (not in E. coli). As the name implies, bacterial bc₁ is similar to mitochondrial bc₁ (Complex III).

Cytochrome electron carriers

Cytochromes are proteins that contain iron. They are found in two very different environments.

Some cytochromes are water-soluble carriers that shuttle electrons to and from large, immobile macromolecular structures imbedded in the membrane. The mobile cytochrome electron carrier in mitochondria is cytochrome c. Bacteria use a number of different mobile cytochrome electron carriers.

Other cytochromes are found within macromolecules such as Complex III and Complex IV. They also function as electron carriers, but in a very different, intramolecular, solid-state environment.

Electrons may enter an electron transport chain at the level of a mobile cytochrome or quinone carrier. For example, electrons from inorganic electron donors (nitrite, ferrous iron, electron transport chain) enter the electron transport chain at the cytochrome level. When electrons enter at a redox level greater than NADH, the electron transport chain must operate in reverse to produce this necessary, higher-energy molecule.

It has been observed that inter-protein electron transport between cytochromes c and c₁ (complex III) depends on pH and the presence of oxygen, suggesting that protons and superoxide may act as redox mediators in the long-distance electron transport process through the aqueous solution.

Electron acceptors and terminal oxidase/reductase

As there are a number of different electron donors (organic matter in organotrophs, inorganic matter in lithotrophs), there are a number of different electron acceptors, both organic and inorganic. As with other steps of the ETC, an enzyme is required to help with the process.

If oxygen is available, it is most often used as the terminal electron acceptor in aerobic bacteria and facultative anaerobes. An oxidase reduces the O₂ to water while oxidizing something else. In mitochondria, the terminal membrane complex (Complex IV) is cytochrome oxidase, which oxidizes the cytochrome. Aerobic bacteria use a number of different terminal oxidases. For example, E. coli (a facultative anaerobe) does not have a cytochrome oxidase or a bc₁ complex. Under aerobic conditions, it uses two different terminal quinol oxidases (both proton pumps) to reduce oxygen to water.

Bacterial terminal oxidases can be split into classes according to the molecules act as terminal electron acceptors. Class I oxidases are cytochrome oxidases and use oxygen as the terminal electron acceptor. Class II oxidases are quinol oxidases and can use a variety of terminal electron acceptors. Both of these classes can be subdivided into categories based on what redox-active components they contain. E.g. Heme aa3 Class 1 terminal oxidases are much more efficient than Class 2 terminal oxidases.

Mostly in anaerobic environments different electron acceptors are used, including nitrate, nitrite, ferric iron, sulfate, carbon dioxide, and small organic molecules such as fumarate. When bacteria grow in anaerobic environments, the terminal electron acceptor is reduced by an enzyme called a reductase. E. coli can use fumarate reductase, nitrate reductase, nitrite reductase, DMSO reductase, or trimethylamine-N-oxide reductase, depending on the availability of these acceptors in the environment.

Most terminal oxidases and reductases are inducible. They are synthesized by the organism as needed, in response to specific environmental conditions.

Photosynthesis

Further information: Light-dependent reaction and Photosynthetic reaction center

Photosynthetic electron transport chain of the thylakoid membrane.

In oxidative phosphorylation, electrons are transferred from an electron donor such as NADH to an acceptor such as O₂ through an electron transport chain, releasing energy. In photophosphorylation, the energy of sunlight is used to create a high-energy electron donor which can subsequently reduce oxidized components and couple to ATP synthesis via proton translocation by the electron transport chain.

Photosynthetic electron transport chains, like the mitochondrial chain, can be considered as a special case of the bacterial systems. They use mobile, lipid-soluble quinone carriers (phylloquinone and plastoquinone) and mobile, water-soluble carriers (cytochromes). They also contain a proton pump. The proton pump in all photosynthetic chains resembles mitochondrial Complex III. The commonly held theory of symbiogenesis proposes that both organelles descended from bacteria.