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is measured), coulometry (the transferred charge is measured over time), amperometry (the cell's current is measured over time), and voltammetry (the cell's current is measured while actively altering the cell's potential). Potentiometry measures the cell's potential, coulometry measures the cell's current, and voltammetry measures the change in current when cell potential changes. === Thermal analysis === Calorimetry and thermogravimetric analysis measure the interaction of a material and heat. === Separation === Separation processes are used to decrease the complexity of material mixtures. Chromatography, electrophoresis and field flow fractionation are representative of this field. ==== Chromatographic assays ==== Chromatography can be used to determine the presence of substances in a sample as different components in a mixture have different tendencies to adsorb onto the stationary phase or dissolve in the mobile phase. Thus, different components of the mixture move at different speed. Different components of a mixture can therefore be identified by their respective Rƒ values, which is the ratio between the migration distance of the substance and the migration distance of the solvent front during chromatography. In combination with the instrumental methods, chromatography can be used in quantitative determination of the substances. Chromatography separates the analyte from the rest of the sample so that it may be measured without interference from other compounds. There are different types of chromatography that differ from the media they use to separate the analyte and the sample. In Thin-layer chromatography, the analyte mixture moves up and separates along the coated sheet under the volatile mobile phase. In Gas chromatography, gas separates the volatile analytes. A common method for chromatography using liquid as a mobile phase is High-performance liquid chromatography. === Hybrid techniques === Combinations of the above techniques produce a "hybrid" or "hyphenated" technique. Several examples are in popular use today and new hybrid
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techniques are under development. For example, gas chromatography-mass spectrometry, gas chromatography-infrared spectroscopy, liquid chromatography-mass spectrometry, liquid chromatography-NMR spectroscopy, liquid chromatography-infrared spectroscopy, and capillary electrophoresis-mass spectrometry. Hyphenated separation techniques refer to a combination of two (or more) techniques to detect and separate chemicals from solutions. Most often the other technique is some form of chromatography. Hyphenated techniques are widely used in chemistry and biochemistry. A slash is sometimes used instead of hyphen, especially if the name of one of the methods contains a hyphen itself. === Microscopy === The visualization of single molecules, single cells, biological tissues, and nanomaterials is an important and attractive approach in analytical science. Also, hybridization with other traditional analytical tools is revolutionizing analytical science. Microscopy can be categorized into three different fields: optical microscopy, electron microscopy, and scanning probe microscopy. Recently, this field is rapidly progressing because of the rapid development of the computer and camera industries. === Lab-on-a-chip === Devices that integrate (multiple) laboratory functions on a single chip of only millimeters to a few square centimeters in size and that are capable of handling extremely small fluid volumes down to less than picoliters. == Errors == Error can be defined as numerical difference between observed value and true value. The experimental error can be divided into two types, systematic error and random error. Systematic error results from a flaw in equipment or the design of an experiment while random error results from uncontrolled or uncontrollable variables in the experiment. In error the true value and observed value in chemical analysis can be related with each other by the equation ε a = | x − x ¯ | {\displaystyle \varepsilon _{\rm {a}}=|x-{\bar {x}}|} where ε a {\displaystyle \varepsilon _{\rm {a}}} is the absolute error. x {\displaystyle x} is the true value. x ¯ {\displaystyle
|
{
"page_id": 2408,
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{\bar {x}}} is the observed value. An error of a measurement is an inverse measure of accurate measurement, i.e. smaller the error greater the accuracy of the measurement. Errors can be expressed relatively. Given the relative error( ε r {\displaystyle \varepsilon _{\rm {r}}} ): ε r = ε a | x | = | x − x ¯ x | {\displaystyle \varepsilon _{\rm {r}}={\frac {\varepsilon _{\rm {a}}}{|x|}}=\left|{\frac {x-{\bar {x}}}{x}}\right|} The percent error can also be calculated: ε r × 100 % {\displaystyle \varepsilon _{\rm {r}}\times 100\%} If we want to use these values in a function, we may also want to calculate the error of the function. Let f {\displaystyle f} be a function with N {\displaystyle N} variables. Therefore, the propagation of uncertainty must be calculated in order to know the error in f {\displaystyle f} : ε a ( f ) ≈ ∑ i = 1 N | ∂ f ∂ x i | ε a ( x i ) = | ∂ f ∂ x 1 | ε a ( x 1 ) + | ∂ f ∂ x 2 | ε a ( x 2 ) + … + | ∂ f ∂ x N | ε a ( x N ) {\displaystyle \varepsilon _{\rm {a}}(f)\approx \sum _{i=1}^{N}\left|{\frac {\partial f}{\partial x_{i}}}\right|\varepsilon _{\rm {a}}(x_{i})=\left|{\frac {\partial f}{\partial x_{1}}}\right|\varepsilon _{\rm {a}}(x_{1})+\left|{\frac {\partial f}{\partial x_{2}}}\right|\varepsilon _{\rm {a}}(x_{2})+\ldots +\left|{\frac {\partial f}{\partial x_{N}}}\right|\varepsilon _{\rm {a}}(x_{N})} == Standards == === Standard curve === A general method for analysis of concentration involves the creation of a calibration curve. This allows for the determination of the amount of a chemical in a material by comparing the results of an unknown sample to those of a series of known standards. If the concentration of element or compound in a sample is too high for the detection
|
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range of the technique, it can simply be diluted in a pure solvent. If the amount in the sample is below an instrument's range of measurement, the method of addition can be used. In this method, a known quantity of the element or compound under study is added, and the difference between the concentration added and the concentration observed is the amount actually in the sample. === Internal standards === Sometimes an internal standard is added at a known concentration directly to an analytical sample to aid in quantitation. The amount of analyte present is then determined relative to the internal standard as a calibrant. An ideal internal standard is an isotopically enriched analyte which gives rise to the method of isotope dilution. === Standard addition === The method of standard addition is used in instrumental analysis to determine the concentration of a substance (analyte) in an unknown sample by comparison to a set of samples of known concentration, similar to using a calibration curve. Standard addition can be applied to most analytical techniques and is used instead of a calibration curve to solve the matrix effect problem. == Signals and noise == One of the most important components of analytical chemistry is maximizing the desired signal while minimizing the associated noise. The analytical figure of merit is known as the signal-to-noise ratio (S/N or SNR). Noise can arise from environmental factors as well as from fundamental physical processes. === Thermal noise === Thermal noise results from the motion of charge carriers (usually electrons) in an electrical circuit generated by their thermal motion. Thermal noise is white noise meaning that the power spectral density is constant throughout the frequency spectrum. The root mean square value of the thermal noise in a resistor is given by v R M S =
|
{
"page_id": 2408,
"source": null,
"title": "Analytical chemistry"
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4 k B T R Δ f , {\displaystyle v_{\rm {RMS}}={\sqrt {4k_{\rm {B}}TR\Delta f}},} where kB is the Boltzmann constant, T is the temperature, R is the resistance, and Δ f {\displaystyle \Delta f} is the bandwidth of the frequency f {\displaystyle f} . === Shot noise === Shot noise is a type of electronic noise that occurs when the finite number of particles (such as electrons in an electronic circuit or photons in an optical device) is small enough to give rise to statistical fluctuations in a signal. Shot noise is a Poisson process, and the charge carriers that make up the current follow a Poisson distribution. The root mean square current fluctuation is given by i R M S = 2 e I Δ f {\displaystyle i_{\rm {RMS}}={\sqrt {2eI\Delta f}}} where e is the elementary charge and I is the average current. Shot noise is white noise. === Flicker noise === Flicker noise is electronic noise with a 1/ƒ frequency spectrum; as f increases, the noise decreases. Flicker noise arises from a variety of sources, such as impurities in a conductive channel, generation, and recombination noise in a transistor due to base current, and so on. This noise can be avoided by modulation of the signal at a higher frequency, for example, through the use of a lock-in amplifier. === Environmental noise === Environmental noise arises from the surroundings of the analytical instrument. Sources of electromagnetic noise are power lines, radio and television stations, wireless devices, compact fluorescent lamps and electric motors. Many of these noise sources are narrow bandwidth and, therefore, can be avoided. Temperature and vibration isolation may be required for some instruments. === Noise reduction === Noise reduction can be accomplished either in computer hardware or software. Examples of hardware noise reduction are the use
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"page_id": 2408,
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of shielded cable, analog filtering, and signal modulation. Examples of software noise reduction are digital filtering, ensemble average, boxcar average, and correlation methods. == Applications == Analytical chemistry has applications including in forensic science, bioanalysis, clinical analysis, environmental analysis, and materials analysis. Analytical chemistry research is largely driven by performance (sensitivity, detection limit, selectivity, robustness, dynamic range, linear range, accuracy, precision, and speed), and cost (purchase, operation, training, time, and space). Among the main branches of contemporary analytical atomic spectrometry, the most widespread and universal are optical and mass spectrometry. In the direct elemental analysis of solid samples, the new leaders are laser-induced breakdown and laser ablation mass spectrometry, and the related techniques with transfer of the laser ablation products into inductively coupled plasma. Advances in design of diode lasers and optical parametric oscillators promote developments in fluorescence and ionization spectrometry and also in absorption techniques where uses of optical cavities for increased effective absorption pathlength are expected to expand. The use of plasma- and laser-based methods is increasing. An interest towards absolute (standardless) analysis has revived, particularly in emission spectrometry. Great effort is being put into shrinking the analysis techniques to chip size. Although there are few examples of such systems competitive with traditional analysis techniques, potential advantages include size/portability, speed, and cost. (micro total analysis system (μTAS) or lab-on-a-chip). Microscale chemistry reduces the amounts of chemicals used. Many developments improve the analysis of biological systems. Examples of rapidly expanding fields in this area are genomics, DNA sequencing and related research in genetic fingerprinting and DNA microarray; proteomics, the analysis of protein concentrations and modifications, especially in response to various stressors, at various developmental stages, or in various parts of the body, metabolomics, which deals with metabolites; transcriptomics, including mRNA and associated fields; lipidomics - lipids and its associated
|
{
"page_id": 2408,
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fields; peptidomics - peptides and its associated fields; and metallomics, dealing with metal concentrations and especially with their binding to proteins and other molecules. Analytical chemistry has played a critical role in the understanding of basic science to a variety of practical applications, such as biomedical applications, environmental monitoring, quality control of industrial manufacturing, forensic science, and so on. The recent developments in computer automation and information technologies have extended analytical chemistry into a number of new biological fields. For example, automated DNA sequencing machines were the basis for completing human genome projects leading to the birth of genomics. Protein identification and peptide sequencing by mass spectrometry opened a new field of proteomics. In addition to automating specific processes, there is effort to automate larger sections of lab testing, such as in companies like Emerald Cloud Lab and Transcriptic. Analytical chemistry has been an indispensable area in the development of nanotechnology. Surface characterization instruments, electron microscopes and scanning probe microscopes enable scientists to visualize atomic structures with chemical characterizations. == See also == Calorimeter Clinical chemistry Environmental chemistry Ion beam analysis List of chemical analysis methods Important publications in analytical chemistry List of materials analysis methods Measurement uncertainty Metrology Microanalysis Nuclear reaction analysis Quality of analytical results Radioanalytical chemistry Rutherford backscattering spectroscopy Sensory analysis - in the field of Food science Virtual instrumentation Working range == References == == Further reading == == External links == Infografik and animation showing the progress of analytical chemistry aas Atomic Absorption Spectrophotometer
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"page_id": 2408,
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The Institute of Predictive and Personalized Medicine of Cancer (IMPPC) (Barcelona) is located in Badalona as a research institute set up by the Consejo Superior de Investigaciones Científicas (CSIC), the Universitat Autònoma de Barcelona (UAB), the City Council of Badalona, the Catalan Institute of Health (ICS), The Germans Trias i Pujol University Hospital (HUGTiP) and the Institute for Health Science Research Germans Trias i Pujol (FIICSGTiP). The IMPCC is adjacent to the Institute for Health Science Research Germans Trias i Pujol. The mission of the IMPPC is to identify the molecular patterns that are predictors of the development of a cancer and can inform its personalized treatment. == References == == External links == IMPPC home page. FIICSGTiP home page.
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{
"page_id": 31721834,
"source": null,
"title": "Institute of Predictive and Personalized Medicine of Cancer"
}
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Analog models of gravity are attempts to model various phenomena of general relativity (e.g., black holes or cosmological geometries) using other physical systems such as waves in a moving fluid and electromagnetic waves in a dielectric medium. These analogs (or analogies) serve to provide new ways of looking at problems, permit ideas from other realms of science to be applied, and may create opportunities for practical experiments within the analog that can be applied back to the source phenomena. Analog models of gravity have been used in hundreds of published articles in the last decade. == Bose-Einstein condensates == It has been shown that Bose-Einstein condensates (BEC) are a good platform to study analog gravity. Rotating blackholes described by Kerr metric have been implemented in a BEC of exciton-polaritons (a quantum fluid of light). == Gravity waves == Gravity waves have been recognized as a promising system for studying analog gravity models. Recent experiments have demonstrated that these waves can effectively simulate phase space horizons, drawing parallels to black hole physics. Specifically, the use of surface gravity water waves has enabled the observation of logarithmic phase singularities and the onset of Fermi–Dirac statistics, phenomena typically associated with quantum systems and gravitational theories. This approach provides valuable insights into the analogies between classical wave systems and quantum mechanical behaviors, expanding the possibilities for exploring gravitational analogs in a controlled laboratory environment. == See also == Acoustic metric Transformation optics Optical metric#Analogue gravity Optical black hole Sonic black hole == References ==
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{
"page_id": 7670122,
"source": null,
"title": "Analog models of gravity"
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The mutation accumulation theory of aging was first proposed by Peter Medawar in 1952 as an evolutionary explanation for biological aging and the associated decline in fitness that accompanies it. Medawar used the term 'senescence' to refer to this process. The theory explains that, in the case where harmful mutations are only expressed later in life, when reproduction has ceased and future survival is increasingly unlikely, then these mutations are likely to be unknowingly passed on to future generations. In this situation the force of natural selection will be weak, and so insufficient to consistently eliminate these mutations. Medawar posited that over time these mutations would accumulate due to genetic drift and lead to the evolution of what is now referred to as aging. == Background and history == Despite Charles Darwin's completion of his theory of biological evolution in the 19th century, the modern logical framework for evolutionary theories of aging wouldn't emerge until almost a century later. Though August Weismann did propose his theory of programmed death, it was met with criticism and never gained mainstream attention. It wasn't until 1930 that Ronald Fisher first noted the conceptual insight which prompted the development of modern aging theories. This concept, namely that the force of natural selection on an individual decreases with age, was analysed further by J. B. S. Haldane, who suggested it as an explanation for the relatively high prevalence of Huntington's disease despite the autosomal dominant nature of the mutation. Specifically, as Huntington's only presents after the age of 30, the force of natural selection against it would have been relatively low in pre-modern societies. It was based on the ideas of Fisher and Haldane that Peter Medawar was able to work out the first complete model explaining why aging occurs, which he presented in a
|
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"page_id": 60885357,
"source": null,
"title": "Mutation accumulation theory"
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|
lecture in 1951 and then published in 1952 == Mechanism of action == Amongst almost all populations, the likelihood that an individual will reproduce is related directly to their age. Starting at 0 at birth, the probability increases to its maximum in young adulthood once sexual maturity has been reached, before gradually decreasing with age. This decrease is caused by the increasing likelihood of death due to external pressures such as predation or illness, as well as the internal pressures inherent to organisms that experience senescence. In such cases deleterious mutations which are expressed early on are strongly selected against due to their major impact on the number of offspring produced by that individual. Mutations that present later in life, by contrast, are relatively unaffected by selective pressure, as their carriers have already passed on their genes, assuming they survive long enough for the mutation to be expressed at all. The result, as predicted by Medawar, is that deleterious late-life mutations will accumulate and result in the evolution of aging as it is known colloquially. This concept is portrayed graphically by Medawar through the concept of a "selection shadow". The shaded region represents the 'shadow' of time during which selective pressure has no effect. Mutations that are expressed within this selection shadow will remain as long as reproductive probability within that age range remains low. == Evidence supporting the mutation accumulation theory == === Predation and Delayed Senescence === In populations where extrinsic mortality is low, the drop in reproductive probability after maturity is less severe than in other cases. The mutation accumulation theory therefore predicts that such populations would evolve delayed senescence. One such example of this scenario can be seen when comparing birds to organisms of equivalent size. It has been suggested that their ability to fly, and
|
{
"page_id": 60885357,
"source": null,
"title": "Mutation accumulation theory"
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|
therefore lower relative risk of predation, is the cause of their longer than expected life span. The implication that flight, and therefore lower predation, increases lifespan is further born out by the fact that bats live on average 3 times longer than similarly sized mammals with comparable metabolic rates. Providing further evidence, insect populations are known to experience very high rates of extrinsic mortality, and as such would be expected to experience rapid senescence and short life spans. The exception to this rule, however, is found in the longevity of eusocial insect queens. As expected when applying the mutation accumulation theory, established queens are at almost no risk of predation or other forms of extrinsic mortality, and consequently age far more slowly than others of their species. === Age-specific reproductive success of Drosophila Melanogaster === In the interest of finding specific evidence for the mutation accumulation theory, separate from that which also supports the similar antagonistic pleiotropy hypothesis, an experiment was conducted involving the breeding of successive generations of Drosophila Melanogaster. Genetic models predict that, in the case of mutation accumulation, elements of fitness, such as reproductive success and survival, will show age-related increases in dominance, homozygous genetic variance and additive variance. Inbreeding depression will also increase with age. This is because these variables are proportional to the equilibrium frequencies of deleterious alleles, which are expected to increase with age under mutation accumulation but not under the antagonistic pleiotropy hypothesis. This was tested experimentally by measuring age specific reproductive success in 100 different genotypes of Drosophila Melanogaster, with findings ultimately supporting the mutation accumulation theory of aging. == Criticisms of the mutation accumulation theory == Under most assumptions, the mutation accumulation theory predicts that mortality rates will reach close to 100% shortly after reaching post-reproductive age. Experimental populations of Drosophila
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{
"page_id": 60885357,
"source": null,
"title": "Mutation accumulation theory"
}
|
Melanogaster, and other organisms, however, exhibit age-specific mortality rates that plateau well before reaching 100%, making mutation accumulation alone an insufficient explanation. It is suggested instead that mutation accumulation is only one factor among many, which together form the cause of aging. In particular, the mutation accumulation theory, the antagonistic pleiotropy hypothesis and the disposable soma theory of aging are all believed to contribute in some way to senescence. == References ==
|
{
"page_id": 60885357,
"source": null,
"title": "Mutation accumulation theory"
}
|
The Sakurai reaction (also known as the Hosomi–Sakurai reaction) is the chemical reaction of carbon electrophiles (such as a ketone shown here) with allyltrimethylsilane catalyzed by strong Lewis acids. The reaction achieves results similar to the addition of an allyl Grignard reagent to the carbonyl. Strong Lewis acids such as titanium tetrachloride, boron trifluoride, tin tetrachloride, and AlCl(Et)2 are all effective in promoting the Sakurai reaction. The reaction involves electrophilic allyl shift via a beta-silyl carbocationic intermediate, the beta-silicon effect. == Mechanism == Allylation of a carbonyl ketone (compound containing a ketone group and two different functional groups) has been shown. In the given reaction, the electrophilic compound (carbon with a ketone group) is treated with titanium tetrachloride, a strong Lewis acid and allyltrimethylsilane. According to the general principle, the Lewis acid first activates the electrophilic carbon in presence of allyltrimethylsilane which then undergoes nucleophilic attack from electrons on the allylic silane. The silicon plays the key role in stabilizing the carbocation of carbon at the β-position. The Sakurai reaction is also applicable for other functional groups such as enones, where conjugate addition is usually seen. In figure 2, the Sakurai reaction has been shown using a cinnamoyl ketone. This reaction follows the same mechanism as the previous reaction shown here. As displayed in the scheme, the Sakurai reaction is proposed to give a secondary carbocation intermediate. Secondary carbocations are high in energy, however it is stabilized by the silicon substituent ("β-silicon effect", a form of silicon-hyperconjugation). == Literature of historic interest == Sakurai, Hideki; Hosomi, Akira; Kumada, Makoto (1969). "Addition of trichloromethyl radicals to alkenylsilanes". The Journal of Organic Chemistry. 36 (4): 1764–1768. doi:10.1021/jo01258a052. Hosomi, Akíra; Sakurai, Hideki (1976). "Syntheses of γ,δ-unsaturated alcohols from allylsilanes and carbonyl compounds in the presence of titanium tetrachloride". Tetrahedron Letters. 17 (16): 1295–1298.
|
{
"page_id": 3934577,
"source": null,
"title": "Sakurai reaction"
}
|
doi:10.1016/S0040-4039(00)78044-0. ISSN 0040-4039. (Hosomi, Akira; Endo, Masahiko; Sakurai, Hideki (5 September 1976). "Allylsilanes as synthetic intermediates. ii. syntheses of homoallyl ethers from allylsilanes and acetals promoted by titanium tetrachloride". Chemistry Letters. 5 (9): 941–942. doi:10.1246/cl.1976.941. ISSN 0366-7022. Hosomi, Akira; Sakurai, Hideki (1 March 1977). "Chemistry of organosilicon compounds. 99. Conjugate addition of allylsilanes to .alpha.,.beta.-enones. A New method of stereoselective introduction of the angular allyl group in fused cyclic .alpha.,.beta.-enones". Journal of the American Chemical Society. 99 (5): 1673–1675. doi:10.1021/ja00447a080. ISSN 0002-7863. == References == == External links == Hosomi-Sakurai reaction @ www.organic-chemistry.org Akira Hosomi homepage
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{
"page_id": 3934577,
"source": null,
"title": "Sakurai reaction"
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Naphthylamine or aminonaphthalene can refer to either of two isomeric chemical compounds: 1-Naphthylamine (1-aminonaphthalene) 2-Naphthylamine (2-aminonaphthalene)
|
{
"page_id": 3148149,
"source": null,
"title": "Naphthylamine"
}
|
Copernicium is a synthetic chemical element; it has symbol Cn and atomic number 112. Its known isotopes are extremely radioactive, and have only been created in a laboratory. The most stable known isotope, copernicium-285, has a half-life of approximately 30 seconds. Copernicium was first created in February 1996 by the GSI Helmholtz Centre for Heavy Ion Research near Darmstadt, Germany. It was named after the astronomer Nicolaus Copernicus on his 537th anniversary. In the periodic table of the elements, copernicium is a d-block transactinide element and a group 12 element. During reactions with gold, it has been shown to be an extremely volatile element, so much so that it is possibly a gas or a volatile liquid at standard temperature and pressure. Copernicium is calculated to have several properties that differ from its lighter homologues in group 12, zinc, cadmium and mercury; due to relativistic effects, it may give up its 6d electrons instead of its 7s ones, and it may have more similarities to the noble gases such as radon rather than its group 12 homologues. Calculations indicate that copernicium may show the oxidation state +4, while mercury shows it in only one compound of disputed existence and zinc and cadmium do not show it at all. It has also been predicted to be more difficult to oxidize copernicium from its neutral state than the other group 12 elements. Predictions vary on whether solid copernicium would be a metal, semiconductor, or insulator. Copernicium is one of the heaviest elements whose chemical properties have been experimentally investigated. == Introduction == == History == === Discovery === Copernicium was first created on 9 February 1996, at the Gesellschaft für Schwerionenforschung (GSI) in Darmstadt, Germany, by Sigurd Hofmann, Victor Ninov et al. This element was created by firing accelerated zinc-70 nuclei at
|
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"source": null,
"title": "Copernicium"
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a target made of lead-208 nuclei in a heavy ion accelerator. A single atom of copernicium was produced with a mass number of 277. (A second was originally reported, but was found to have been based on data fabricated by Ninov, and was thus retracted.) 20882Pb + 7030Zn → 278112Cn* → 277112Cn + 10n In May 2000, the GSI successfully repeated the experiment to synthesize a further atom of copernicium-277. This reaction was repeated at RIKEN using the Search for a Super-Heavy Element Using a Gas-Filled Recoil Separator set-up in 2004 and 2013 to synthesize three further atoms and confirm the decay data reported by the GSI team. This reaction had also previously been tried in 1971 at the Joint Institute for Nuclear Research in Dubna, Russia to aim for 276Cn (produced in the 2n channel), but without success. The IUPAC/IUPAP Joint Working Party (JWP) assessed the claim of copernicium's discovery by the GSI team in 2001 and 2003. In both cases, they found that there was insufficient evidence to support their claim. This was primarily related to the contradicting decay data for the known nuclide rutherfordium-261. However, between 2001 and 2005, the GSI team studied the reaction 248Cm(26Mg,5n)269Hs, and were able to confirm the decay data for hassium-269 and rutherfordium-261. It was found that the existing data on rutherfordium-261 was for an isomer, now designated rutherfordium-261m. In May 2009, the JWP reported on the claims of discovery of element 112 again and officially recognized the GSI team as the discoverers of element 112. This decision was based on the confirmation of the decay properties of daughter nuclei as well as the confirmatory experiments at RIKEN. Work had also been done at the Joint Institute for Nuclear Research in Dubna, Russia from 1998 to synthesise the heavier isotope 283Cn in
|
{
"page_id": 67958,
"source": null,
"title": "Copernicium"
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the hot fusion reaction 238U(48Ca,3n)283Cn; most observed atoms of 283Cn decayed by spontaneous fission, although an alpha decay branch to 279Ds was detected. While initial experiments aimed to assign the produced nuclide with its observed long half-life of 3 minutes based on its chemical behaviour, this was found to be not mercury-like as would have been expected (copernicium being under mercury in the periodic table), and indeed now it appears that the long-lived activity might not have been from 283Cn at all, but its electron capture daughter 283Rg instead, with a shorter 4-second half-life associated with 283Cn. (Another possibility is assignment to a metastable isomeric state, 283mCn.) While later cross-bombardments in the 242Pu+48Ca and 245Cm+48Ca reactions succeeded in confirming the properties of 283Cn and its parents 287Fl and 291Lv, and played a major role in the acceptance of the discoveries of flerovium and livermorium (elements 114 and 116) by the JWP in 2011, this work originated subsequent to the GSI's work on 277Cn and priority was assigned to the GSI. === Naming === Using Mendeleev's nomenclature for unnamed and undiscovered elements, copernicium should be known as eka-mercury. In 1979, IUPAC published recommendations according to which the element was to be called ununbium (with the corresponding symbol of Uub), a systematic element name as a placeholder, until the element was discovered (and the discovery then confirmed) and a permanent name was decided on. Although widely used in the chemical community on all levels, from chemistry classrooms to advanced textbooks, the recommendations were mostly ignored among scientists in the field, who either called it "element 112", with the symbol of E112, (112), or even simply 112. After acknowledging the GSI team's discovery, the IUPAC asked them to suggest a permanent name for element 112. On 14 July 2009, they proposed copernicium with
|
{
"page_id": 67958,
"source": null,
"title": "Copernicium"
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the element symbol Cp, after Nicolaus Copernicus "to honor an outstanding scientist, who changed our view of the world". During the standard six-month discussion period among the scientific community about the naming, it was pointed out that the symbol Cp was previously associated with the name cassiopeium (cassiopium), now known as lutetium (Lu). Moreover, Cp is frequently used today to mean the cyclopentadienyl ligand (C5H5). Primarily because cassiopeium (Cp) was (until 1949) accepted by IUPAC as an alternative allowed name for lutetium, the IUPAC disallowed the use of Cp as a future symbol, prompting the GSI team to put forward the symbol Cn as an alternative. On 19 February 2010, the 537th anniversary of Copernicus' birth, IUPAC officially accepted the proposed name and symbol. == Isotopes == Copernicium has no stable or naturally occurring isotopes. Several radioactive isotopes have been synthesized in the laboratory, either by fusing two atoms or by observing the decay of heavier elements. Eight different isotopes have been reported with mass numbers 277 and 280–286, and one unconfirmed metastable isomer in 285Cn has been reported. Most of these decay predominantly through alpha decay, but some undergo spontaneous fission, and copernicium-283 may have an electron capture branch. The isotope copernicium-283 was instrumental in the confirmation of the discoveries of the elements flerovium and livermorium. === Half-lives === All confirmed copernicium isotopes are extremely unstable and radioactive; in general, heavier isotopes are more stable than the lighter, and isotopes with an odd neutron number have relatively longer half-lives due to additional hindrance against spontaneous fission. The most stable known isotope, 285Cn, has a half-life of 30 seconds; 283Cn has a half-life of 4 seconds, and the unconfirmed 285mCn and 286Cn have half-lives of about 15 and 8.45 seconds respectively. Other isotopes have half-lives shorter than one second. 281Cn
|
{
"page_id": 67958,
"source": null,
"title": "Copernicium"
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|
and 284Cn both have half-lives on the order of 0.1 seconds, and the remaining isotopes have half-lives shorter than one millisecond. It is predicted that the heavy isotopes 291Cn and 293Cn may have half-lives longer than a few decades, for they are predicted to lie near the center of the theoretical island of stability, and may have been produced in the r-process and be detectable in cosmic rays, though they would be about 10−12 times as abundant as lead. The lightest isotopes of copernicium have been synthesized by direct fusion between two lighter nuclei and as decay products (except for 277Cn, which is not known to be a decay product), while the heavier isotopes are only known to be produced by decay of heavier nuclei. The heaviest isotope produced by direct fusion is 283Cn; the three heavier isotopes, 284Cn, 285Cn, and 286Cn, have only been observed as decay products of elements with larger atomic numbers. In 1999, American scientists at the University of California, Berkeley, announced that they had succeeded in synthesizing three atoms of 293Og. These parent nuclei were reported to have successively emitted three alpha particles to form copernicium-281 nuclei, which were claimed to have undergone alpha decay, emitting alpha particles with decay energy 10.68 MeV and half-life 0.90 ms, but their claim was retracted in 2001 as it had been based on data fabricated by Ninov. This isotope was truly produced in 2010 by the same team; the new data contradicted the previous fabricated data. The missing isotopes 278Cn and 279Cn are too heavy to be produced by cold fusion and too light to be produced by hot fusion. They might be filled from above by decay of heavier elements produced by hot fusion, and indeed 280Cn and 281Cn were produced this way. The isotopes 286Cn and
|
{
"page_id": 67958,
"source": null,
"title": "Copernicium"
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287Cn could be produced by charged-particle evaporation, in the reaction 244Pu(48Ca,αxn) with x equalling 1 or 2. == Predicted properties == Very few properties of copernicium or its compounds have been measured; this is due to its extremely limited and expensive production and the fact that copernicium (and its parents) decays very quickly. A few singular chemical properties have been measured, as well as the boiling point, but properties of the copernicium metal remain generally unknown and for the most part, only predictions are available. === Chemical === Copernicium is the tenth and last member of the 6d series and is the heaviest group 12 element in the periodic table, below zinc, cadmium and mercury. It is predicted to differ significantly from the lighter group 12 elements. The valence s-subshells of the group 12 elements and period 7 elements are expected to be relativistically contracted most strongly at copernicium. This and the closed-shell configuration of copernicium result in it probably being a very noble metal. A standard reduction potential of +2.1 V is predicted for the Cn2+/Cn couple. Copernicium's predicted first ionization energy of 1155 kJ/mol almost matches that of the noble gas xenon at 1170.4 kJ/mol. Copernicium's metallic bonds should also be very weak, possibly making it extremely volatile like the noble gases, and potentially making it gaseous at room temperature. However, it should be able to form metal–metal bonds with copper, palladium, platinum, silver, and gold; these bonds are predicted to be only about 15–20 kJ/mol weaker than the analogous bonds with mercury. In opposition to the earlier suggestion, ab initio calculations at the high level of accuracy predicted that the chemistry of singly-valent copernicium resembles that of mercury rather than that of the noble gases. The latter result can be explained by the huge spin–orbit interaction which
|
{
"page_id": 67958,
"source": null,
"title": "Copernicium"
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significantly lowers the energy of the vacant 7p1/2 state of copernicium. Once copernicium is ionized, its chemistry may present several differences from those of zinc, cadmium, and mercury. Due to the stabilization of 7s electronic orbitals and destabilization of 6d ones caused by relativistic effects, Cn2+ is likely to have a [Rn]5f146d87s2 electronic configuration, using the 6d orbitals before the 7s one, unlike its homologues. The fact that the 6d electrons participate more readily in chemical bonding means that once copernicium is ionized, it may behave more like a transition metal than its lighter homologues, especially in the possible +4 oxidation state. In aqueous solutions, copernicium may form the +2 and perhaps +4 oxidation states. The diatomic ion Hg2+2, featuring mercury in the +1 oxidation state, is well-known, but the Cn2+2 ion is predicted to be unstable or even non-existent. Copernicium(II) fluoride, CnF2, should be more unstable than the analogous mercury compound, mercury(II) fluoride (HgF2), and may even decompose spontaneously into its constituent elements. As the most electronegative reactive element, fluorine may be the only element able to oxidise copernicium even further to the +4 and even +6 oxidation states in CnF4 and CnF6; the latter may require matrix-isolation conditions to be detected, as in the disputed detection of HgF4. CnF4 should be more stable than CnF2. In polar solvents, copernicium is predicted to preferentially form the CnF−5 and CnF−3 anions rather than the analogous neutral fluorides (CnF4 and CnF2, respectively), although the analogous bromide or iodide ions may be more stable towards hydrolysis in aqueous solution. The anions CnCl2−4 and CnBr2−4 should also be able to exist in aqueous solution. The formation of thermodynamically stable copernicium(II) and (IV) fluorides would be analogous to the chemistry of xenon. Analogous to mercury(II) cyanide (Hg(CN)2), copernicium is expected to form a stable
|
{
"page_id": 67958,
"source": null,
"title": "Copernicium"
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cyanide, Cn(CN)2. === Physical and atomic === Copernicium should be a dense metal, with a density of 14.0 g/cm3 in the liquid state at 300 K; this is similar to the known density of mercury, which is 13.534 g/cm3. (Solid copernicium at the same temperature should have a higher density of 14.7 g/cm3.) This results from the effects of copernicium's higher atomic weight being cancelled out by its larger interatomic distances compared to mercury. Some calculations predicted copernicium to be a gas at room temperature due to its closed-shell electron configuration, which would make it the first gaseous metal in the periodic table. A 2019 calculation agrees with these predictions on the role of relativistic effects, suggesting that copernicium will be a volatile liquid bound by dispersion forces under standard conditions. Its melting point is estimated at 283±11 K and its boiling point at 340±10 K, the latter in agreement with the experimentally estimated value of 357+112−108 K. The atomic radius of copernicium is expected to be around 147 pm. Due to the relativistic stabilization of the 7s orbital and destabilization of the 6d orbital, the Cn+ and Cn2+ ions are predicted to give up 6d electrons instead of 7s electrons, which is the opposite of the behavior of its lighter homologues. In addition to the relativistic contraction and binding of the 7s subshell, the 6d5/2 orbital is expected to be destabilized due to spin–orbit coupling, making it behave similarly to the 7s orbital in terms of size, shape, and energy. Predictions of the expected band structure of copernicium are varied. Calculations in 2007 expected that copernicium may be a semiconductor with a band gap of around 0.2 eV, crystallizing in the hexagonal close-packed crystal structure. However, calculations in 2017 and 2018 suggested that copernicium should be a noble metal
|
{
"page_id": 67958,
"source": null,
"title": "Copernicium"
}
|
at standard conditions with a body-centered cubic crystal structure: it should hence have no band gap, like mercury, although the density of states at the Fermi level is expected to be lower for copernicium than for mercury. 2019 calculations then suggested that in fact copernicium has a large band gap of 6.4 ± 0.2 eV, which should be similar to that of the noble gas radon (predicted as 7.1 eV) and would make it an insulator; bulk copernicium is predicted by these calculations to be bound mostly by dispersion forces, like the noble gases. Like mercury, radon, and flerovium, but not oganesson (eka-radon), copernicium is calculated to have no electron affinity. == Experimental atomic gas phase chemistry == Interest in copernicium's chemistry was sparked by predictions that it would have the largest relativistic effects in the whole of period 7 and group 12, and indeed among all 118 known elements. Copernicium is expected to have the ground state electron configuration [Rn] 5f14 6d10 7s2 and thus should belong to group 12 of the periodic table, according to the Aufbau principle. As such, it should behave as the heavier homologue of mercury and form strong binary compounds with noble metals like gold. Experiments probing the reactivity of copernicium have focused on the adsorption of atoms of element 112 onto a gold surface held at varying temperatures, in order to calculate an adsorption enthalpy. Owing to relativistic stabilization of the 7s electrons, copernicium shows radon-like properties. Experiments were performed with the simultaneous formation of mercury and radon radioisotopes, allowing a comparison of adsorption characteristics. The first chemical experiments on copernicium were conducted using the 238U(48Ca,3n)283Cn reaction. Detection was by spontaneous fission of the claimed parent isotope with half-life of 5 minutes. Analysis of the data indicated that copernicium was more volatile than
|
{
"page_id": 67958,
"source": null,
"title": "Copernicium"
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|
mercury and had noble gas properties. However, the confusion regarding the synthesis of copernicium-283 has cast some doubt on these experimental results. Given this uncertainty, between April–May 2006 at the JINR, a FLNR–PSI team conducted experiments probing the synthesis of this isotope as a daughter in the nuclear reaction 242Pu(48Ca,3n)287Fl. (The 242Pu + 48Ca fusion reaction has a slightly larger cross-section than the 238U + 48Ca reaction, so that the best way to produce copernicium for chemical experimentation is as an overshoot product as the daughter of flerovium.) In this experiment, two atoms of copernicium-283 were unambiguously identified and the adsorption properties were interpreted to show that copernicium is a more volatile homologue of mercury, due to formation of a weak metal-metal bond with gold. This agrees with general indications from some relativistic calculations that copernicium is "more or less" homologous to mercury. However, it was pointed out in 2019 that this result may simply be due to strong dispersion interactions. In April 2007, this experiment was repeated and a further three atoms of copernicium-283 were positively identified. The adsorption property was confirmed and indicated that copernicium has adsorption properties in agreement with being the heaviest member of group 12. These experiments also allowed the first experimental estimation of copernicium's boiling point: 84+112−108 °C, so that it may be a gas at standard conditions. Because the lighter group 12 elements often occur as chalcogenide ores, experiments were conducted in 2015 to deposit copernicium atoms on a selenium surface to form copernicium selenide, CnSe. Reaction of copernicium atoms with trigonal selenium to form a selenide was observed, with -ΔHadsCn(t-Se) > 48 kJ/mol, with the kinetic hindrance towards selenide formation being lower for copernicium than for mercury. This was unexpected as the stability of the group 12 selenides tends to decrease down
|
{
"page_id": 67958,
"source": null,
"title": "Copernicium"
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|
the group from ZnSe to HgSe. == See also == Island of stability == Notes == == References == == Bibliography == Audi, G.; Kondev, F. G.; Wang, M.; Huang, W. J.; Naimi, S. (2017). "The NUBASE2016 evaluation of nuclear properties". Chinese Physics C. 41 (3). 030001. Bibcode:2017ChPhC..41c0001A. doi:10.1088/1674-1137/41/3/030001. Beiser, A. (2003). Concepts of modern physics (6th ed.). McGraw-Hill. ISBN 978-0-07-244848-1. OCLC 48965418. Hoffman, D. C.; Ghiorso, A.; Seaborg, G. T. (2000). The Transuranium People: The Inside Story. World Scientific. ISBN 978-1-78-326244-1. Kragh, H. (2018). From Transuranic to Superheavy Elements: A Story of Dispute and Creation. Springer. ISBN 978-3-319-75813-8. Zagrebaev, Valeriy; Karpov, Alexander; Greiner, Walter (2013). "Future of superheavy element research: Which nuclei could be synthesized within the next few years?" (PDF). 11th International Conference on Nucleus-Nucleus Collisions (NN2012). Journal of Physics: Conference Series. Vol. 420. IOP Publishing. doi:10.1088/1742-6596/420/1/012001. Retrieved 20 August 2013. == External links == Copernicium at The Periodic Table of Videos (University of Nottingham)
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{
"page_id": 67958,
"source": null,
"title": "Copernicium"
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The United Nations General Assembly had declared 2011–20 the United Nations Decade on Biodiversity (Resolution 65/161). The UN Decade on Biodiversity had served to support and promote implementation of the Strategic Plan for Biodiversity and the Aichi Biodiversity Targets, with the goal of significantly reducing biodiversity loss. None of the 20 aichi targets were achieved, though progress was made towards several of them. == Background == On December 22, 2010, building on the International Year of Biodiversity (2010) and the goal of significantly reducing biodiversity loss, the United Nations General Assembly declared 2011–2020 the United Nations Decade on Biodiversity (Resolution 65/161). == Aims == The UN Decade on Biodiversity served to support and promote the implementation of the objectives of the Strategic Plan for Biodiversity and the Aichi Biodiversity Targets, which were adopted in 2010, at the 10th Conference of the Parties to the CBD, held in Aichi, Japan. Throughout the UN Decade on Biodiversity, governments were encouraged to develop, implement and communicate the results of national strategies for implementation of the Strategic Plan for Biodiversity. It also sought to promote the involvement of a variety of national and intergovernmental factors and other stakeholders in the goal of mainstreaming biodiversity into broader development planning and economic activities. The aim was to place special focus on supporting actions that address the underlying causes of biodiversity loss, including production and consumption patterns. The Decade was to be succeeded by the Post-2020 Biodiversity Framework, which is itself a stepping stone to the 2050 Vision of "Living in harmony with nature", which envisages that "By 2050, biodiversity is valued, conserved, restored and wisely used, maintaining ecosystem services, sustaining a healthy planet and delivering benefits essential for all people." == Outcomes == On 30 September 2020, world leaders virtually gathered at the first ever global
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{
"page_id": 31590777,
"source": null,
"title": "United Nations Decade on Biodiversity"
}
|
Summit on Biodiversity. The summit involved pre-recorded statements from over 100 states and organizations. It was intended to build momentum for the fifteenth Conference of the Parties to the United Nations Convention on Biodiversity, which was postponed to 2021 due to the coronavirus. Many speakers acknowledged that none of the Aichi Biodiversity Targets established in 2010 were met during the United Nations Decade on Biodiversity. Of the 60 sub goals used to monitor progress towards the archi goals, 7 were achieved, with progress made on another 38. The decade was followed by the UN Decade on Ecosystem Restoration, which aims to drastically scale up the restoration of degraded and destroyed ecosystems. == See also == Convention on Biological Diversity International Day for Biological Diversity International Year of Biodiversity (2010) International Year of Forests (2011) == References == The information above, for the most part, is based on the official websites of the Convention on Biological Diversity and of the United Nations Decade on Biodiversity. == External links == United Nations Decade on Biodiversity United Nations Decade on Biodiversity on Facebook Convention on Biological Diversity Strategic Plan
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{
"page_id": 31590777,
"source": null,
"title": "United Nations Decade on Biodiversity"
}
|
Subterranean fauna refers to animal species that are adapted to live in an underground environment. Troglofauna and stygofauna are the two types of subterranean fauna. Both are associated with hypogeal habitats – troglofauna is associated with terrestrial subterranean environment (caves and underground spaces above the water table), and stygofauna with all kind of subterranean waters (groundwater, aquifers, subterranean rivers, dripping bowls, gours, etc.). == Environment == Subterranean fauna is found worldwide and includes representatives of many animal groups, mostly arthropods and other invertebrates. However, there is a number of vertebrates (such as cavefishes and cave salamanders), although they are less common. Because of the complexity in exploring underground environments, many subterranean species are yet to be discovered and described. Peculiarities of underground habitat make it an extreme environment and, consequently, underground species are usually less than species living in epigean habitats. The main characteristic of underground environment is the lack of sunlight. Climatic values, like temperature and relative humidity, are generally almost stable – temperature corresponds to annual mean temperature in the place where the cavity opens, relative humidity rarely drops below 90%. Food sources are limited and localized. The lack of sunlight inhibits photosynthetic processes, so food comes only from epigean environment (through percolating water, gravity, or passive transport by animals). An exception are caves like the Movile Cave, where chemosynthesis forms the foundation of the food chain. Caves that are close to the surface, such as lava tubes, often have tree roots hanging from the cave roof, which provide nutrients for sap-feeding insects. Other important food sources in underground habitats are animals being decomposed and bat guano, that creates large invertebrate communities in such caves. == Ecological classification == Cave dwelling animals show different levels of adaptations to underground environment. According to a recent classification, animals living in
|
{
"page_id": 39651706,
"source": null,
"title": "Subterranean fauna"
}
|
terrestrial subterranean habitats can be classified into 3 categories, based on their ecology: troglobionts (or troglobites): species strongly bound to subterranean habitats; troglophiles: species living both in subterranean and in epigean habitats. Troglophiles are also divided in eutroglophiles (epigean species able to maintain a permanent subterranean population) and subtroglophiles (species inclined to perpetually or temporarily inhabit a subterranean habitat, but intimately associated with epigean habitats for some functions); trogloxenes: species only occurring sporadically in a hypogean habitat and unable to establish a subterranean population. Regarding stygofauna, the corresponding words stygobionts (or stygobites), stygophiles and stygoxenes are used. == Biology == Characteristics of underground environment caused cave dwelling animals to evolve a number of adaptations, both morphological and physiological. Examples of morphological adaptations include depigmentation (loss of external pigmentation), a reduction of cuticle thickness and the often extreme decrease of eyesight culminating in anophthalmia (complete loss of eyes). Exceptions, however, are harvestmen (Opiliones) in New Zealand caves, which possess large, functional eyes, presumably because these spider-like chelicerates feed on cave-dwelling, light-emitting glowworm larvae Arachnocampa which they detect visually. Other adaptations include the development and elongation of antennal and locomotory appendages, in order to better move around and respond to environmental stimuli. These structures are well endowed with chemical, tactile and humidity receptors (such as Hamann's organ in the cave beetle Leptodirus hochenwartii). Physiological adaptations include slow metabolism and reduced energy consumption, due to limited food supply and low energy efficiency. This is likely to be realized through reducing movements, erasing aggressive interactions, improving feeding capability and food usage efficiency, and through ectothermy. As a consequence, cave dwelling animals can resist without eating for long time, live more than comparable epigean species, reproduce late in their lifespan, and produce fewer and bigger eggs. == Evolution and ecology == Subterranean fauna have evolved
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{
"page_id": 39651706,
"source": null,
"title": "Subterranean fauna"
}
|
in isolation. Stratigraphic barriers, such as rock walls and layers, and fluvial barriers, such as rivers and streams, prevent or hinder the dispersal of these animals. Consequently, subterranean fauna habitat and food availability can be very disjunct and precludes the great range of observed diversity across landscapes. == Threats to subterranean fauna == Floodwaters can be detrimental to subterranean species, by dramatically changing the availability of habitat, food and connectivity to other habitats and oxygen. Many subterranean fauna are likely to be sensitive to changes in their environment and floods, which can accompany a drop in temperature, may adversely affect some animals. Humans also pose a threat to troglofauna. Mismanagement of contaminants (e.g. pesticides and sewage) may poison subterranean fauna communities and removal of habitat (e.g. rising/lowering of the watertable or various forms of mining) can also be a major threat. == See also == Cave conservation List of troglobites Speleology Subterranean river Trogloxene == References ==
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{
"page_id": 39651706,
"source": null,
"title": "Subterranean fauna"
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|
Electrochemical fluorination (ECF), or electrofluorination, is a foundational organofluorine chemistry method for the preparation of fluorocarbon-based organofluorine compounds. The general approach represents an application of electrosynthesis. The fluorinated chemical compounds produced by ECF are useful because of their distinctive solvation properties and the relative inertness of carbon–fluorine bonds. Two ECF synthesis routes are commercialized and commonly applied: the Simons process and the Phillips Petroleum process. It is also possible to electrofluorinate in various organic media. Prior to the development of these methods, fluorination with fluorine, a dangerous oxidizing agent, was a dangerous and wasteful process. ECF can be cost-effective, but it may also result in low yields. == Simons process == The Simons process, named after Joseph H. Simons entails electrolysis of a solution of an organic compound in a solution of hydrogen fluoride. An individual reaction can be described as: R3C–H + HF → R3C–F + H2 In the course of a typical synthesis, this reaction occurs once for each C–H bond in the precursor. The cell potential is maintained near 5–6 V. The anode is nickel-plated. Simons discovered the process in the 1930s at Pennsylvania State College (U.S.), under the sponsorship of the 3M Corporation. The results were not published until after World War II because the work was classified due to its relevance to the manufacture of uranium hexafluoride. In 1949 Simons and his coworkers published a long paper in the Journal of the Electrochemical Society. The Simons process is used for the production of perfluorinated amines, ethers, carboxylic acids, and sulfonic acids. For carboxylic and sulfonic acids, the products are the corresponding acyl fluorides and sulfonyl fluorides. The method has been adapted to laboratory-scale preparations. Two noteworthy considerations are (i) the hazards associated with hydrogen fluoride (the solvent and fluorine source) and (ii) the requirement for
|
{
"page_id": 20842876,
"source": null,
"title": "Electrochemical fluorination"
}
|
anhydrous conditions. == Phillips Petroleum process == This method is similar to the Simons Process but is typically applied to the preparation from volatile hydrocarbons and chlorohydrocarbons. In this process, electrofluorination is conducted at porous graphite anodes in molten potassium fluoride in hydrogen fluoride. The species KHF2 is relatively low melting, a good electrolyte, and an effective source of fluorine. The technology is sometimes called “CAVE” for Carbon Anode Vapor Phase Electrochemical Fluorination and was widely used at manufacturing sites of the 3M Corporation. The organic compound is fed through a porous anode leading to exchange of fluorine for hydrogen but not chlorine. == Other methods == ECF has also been conducted in organic media, using for example organic salts of fluoride and acetonitrile as the solvent. A typical fluoride source is (C2H5)3N:3HF. In some cases, acetonitrile is omitted, and the solvent and electrolyte are the triethylamine-HF mixture. Representative products of this method are fluorobenzene (from benzene) and 1,2-difluoroalkanes (from alkenes). == References ==
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{
"page_id": 20842876,
"source": null,
"title": "Electrochemical fluorination"
}
|
A gene family is a set of several similar genes, formed by duplication of a single original gene, and generally with similar biochemical functions. One such family are the genes for human hemoglobin subunits; the ten genes are in two clusters on different chromosomes, called the α-globin and β-globin loci. These two gene clusters are thought to have arisen as a result of a precursor gene being duplicated approximately 500 million years ago. Genes are categorized into families based on shared nucleotide or protein sequences. Phylogenetic techniques can be used as a more rigorous test. The positions of exons within the coding sequence can be used to infer common ancestry. Knowing the sequence of the protein encoded by a gene can allow researchers to apply methods that find similarities among protein sequences that provide more information than similarities or differences among DNA sequences. If the genes of a gene family encode proteins, the term protein family is often used in an analogous manner to gene family. The expansion or contraction of gene families along a specific lineage can be due to chance, or can be the result of natural selection. To distinguish between these two cases is often difficult in practice. Recent work uses a combination of statistical models and algorithmic techniques to detect gene families that are under the effect of natural selection. The HUGO Gene Nomenclature Committee (HGNC) creates nomenclature schemes using a "stem" (or "root") symbol for members of a gene family (by homology or function), with a hierarchical numbering system to distinguish the individual members. For example, for the peroxiredoxin family, PRDX is the root symbol, and the family members are PRDX1, PRDX2, PRDX3, PRDX4, PRDX5, and PRDX6. == Basic structure == One level of genome organization is the grouping of genes into several gene families.
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{
"page_id": 526719,
"source": null,
"title": "Gene family"
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Gene families are groups of related genes that share a common ancestor. Members of gene families may be paralogs or orthologs. Gene paralogs are genes with similar sequences from within the same species while gene orthologs are genes with similar sequences in different species. Gene families are highly variable in size, sequence diversity, and arrangement. Depending on the diversity and functions of the genes within the family, families can be classified as multigene families or superfamilies. Multigene families typically consist of members with similar sequences and functions, though a high degree of divergence (at the sequence and/or functional level) does not lead to the removal of a gene from a gene family. Individual genes in the family may be arranged close together on the same chromosome or dispersed throughout the genome on different chromosomes. Due to the similarity of their sequences and their overlapping functions, individual genes in the family often share regulatory control elements. In some instances, gene members have identical (or nearly identical) sequences. Such families allow for massive amounts of gene product to be expressed in a short time as needed. Other families allow for similar but specific products to be expressed in different cell types or at different stages of an organism's development. Superfamilies are much larger than single multigene families. Superfamilies contain up to hundreds of genes, including multiple multigene families as well as single, individual gene members. The large number of members allows superfamilies to be widely dispersed with some genes clustered and some spread far apart. The genes are diverse in sequence and function displaying various levels of expression and separate regulation controls. Some gene families also contain pseudogenes, sequences of DNA that closely resemble established gene sequences but are non-functional. Different types of pseudogenes exist. Non-processed pseudogenes are genes that acquired mutations
|
{
"page_id": 526719,
"source": null,
"title": "Gene family"
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over time becoming non-functional. Processed pseudogenes are genes that have lost their function after being moved around the genome by retrotransposition. Pseudogenes that have become isolated from the gene family they originated in, are referred to as orphans. == Formation == Gene families arose from multiple duplications of an ancestral gene, followed by mutation and divergence. Duplications can occur within a lineage (e.g., humans might have two copies of a gene that is found only once in chimpanzees) or they are the result of speciation. For example, a single gene in the ancestor of humans and chimpanzees now occurs in both species and can be thought of as having been 'duplicated' via speciation. As a result of duplication by speciation, a gene family might include 15 genes, one copy in each of 15 different species. === Duplication === In the formation of gene families, four levels of duplication exist: 1) exon duplication and shuffling, 2) entire gene duplication, 3) multigene family duplication, and 4) whole genome duplication. Exon duplication and shuffling gives rise to variation and new genes. Genes are then duplicated to form multigene families which duplicate to form superfamilies spanning multiple chromosomes. Whole genome duplication doubles the number of copies of every gene and gene family. Whole genome duplication or polyploidization can be either autopolyploidization or alloploidization. Autopolyploidization is the duplication of the same genome and allopolyploidization is the duplication of two closely related genomes or hybridized genomes from different species. Duplication occurs primarily through uneven crossing over events in meiosis of germ cells. (1,2) When two chromosomes misalign, crossing over - the exchange of gene alleles - results in one chromosome expanding or increasing in gene number and the other contracting or decreasing in gene number. The expansion of a gene cluster is the duplication of genes
|
{
"page_id": 526719,
"source": null,
"title": "Gene family"
}
|
that leads to larger gene families. === Relocation === Gene members of a multigene family or multigene families within superfamilies exist on different chromosomes due to relocation of those genes after duplication of the ancestral gene. Transposable elements play a role in the movement of genes. Transposable elements are recognized by inverted repeats at their 5' and 3' ends. When two transposable elements are close enough in the same region on a chromosome, they can form a composite transposon. The protein transposase recognizes the outermost inverted repeats, cutting the DNA segment. Any genes between the two transposable elements are relocated as the composite transposon jumps to a new area of the genome. Reverse transcription is another method of gene movement. An mRNA transcript of a gene is reversed transcribed, or copied, back into DNA. This new DNA copy of the mRNA is integrated into another part of the genome, resulting in gene family members being dispersed. A special type of multigene family is implicated in the movement of gene families and gene family members. LINE (Long INterspersed Elements) and SINE (Short INterspersed Elements) families are highly repetitive DNA sequences spread all throughout the genome. The LINEs contain a sequence that encodes a reverse transcriptase protein. This protein aids in copying the RNA transcripts of LINEs and SINEs back into DNA, and integrates them into different areas of the genome. This self-perpetuates the growth of LINE and SINE families. Due to the highly repetitive nature of these elements, LINEs and SINEs when close together also trigger unequal crossing over events which result in single-gene duplications and the formation of gene families. === Divergence === Non-synonymous mutations resulting in the substitution of amino acids, increase in duplicate gene copies. Duplication gives rise to multiple copies of the same gene, giving a level
|
{
"page_id": 526719,
"source": null,
"title": "Gene family"
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of redundancy where mutations are tolerated. With one functioning copy of the gene, other copies are able to acquire mutations without being extremely detrimental to the organisms. Mutations allow duplicate genes to acquire new or different functions. === Concerted evolution === Some multigene families are extremely homogenous, with individual genes members sharing identical or almost identical sequences. The process by which gene families maintain high homogeneity is Concerted evolution. Concerted evolution occurs through repeated cycles of unequal crossing over events and repeated cycles of gene transfer and conversion. Unequal crossing over leads to the expansion and contraction of gene families. Gene families have an optimal size range that natural selection acts towards. Contraction deletes divergent gene copies and keeps gene families from becoming too large. Expansion replaces lost gene copies and prevents gene families from becoming too small. Repeat cycles of gene transfer and conversion increasingly make gene family members more similar. In the process of gene transfer, allelic gene conversion is biased. Mutant alleles spreading in a gene family towards homogeneity is the same process of an advantageous allele spreading in a population towards fixation. Gene conversion also aids in creating genetic variation in some cases. == Evolution == Gene families, part of a hierarchy of information storage in a genome, play a large role in the evolution and diversity of multicellular organisms. Gene families are large units of information and genetic variability. Over evolutionary time, gene families have expanded and contracted with genes within a family duplicating and diversifying into new genes, and genes being lost. An entire gene family may also be lost, or gained through de novo gene birth, by such extensive divergence such that a gene is considered part of a new family, or by horizontal gene transfer. When the number of genes per genome
|
{
"page_id": 526719,
"source": null,
"title": "Gene family"
}
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remains relatively constant, this implies that genes are gained and lost at relatively same rates. There are some patterns in which genes are more likely to be lost vs. which are more likely to duplicate and diversify into multiple copies. An adaptive expansion of a single gene into many initially identical copies occurs when natural selection would favour additional gene copies. This is the case when an environmental stressor acts on a species. Gene amplification is more common in bacteria and is a reversible process. Contraction of gene families commonly results from accumulation of loss of function mutations. A nonsense mutation which prematurely halts gene transcription becomes fixed in the population, leading to the loss of genes. This process occurs when changes in the environment render a gene redundant. == Functional family == In addition to classification by evolution (structural gene family), the HGNC also makes "gene families" by function in their stem nomenclature. As a result, a stem can also refer to genes that have the same function, often part of the same protein complex. For example, BRCA1 and BRCA2 are unrelated genes that are both named for their role in breast cancer and RPS2 and RPS3 are unrelated ribosomal proteins found in the same small subunit. The HGNC also maintains a "gene group" (formerly "gene family") classification. A gene can be a member of multiple groups, and all groups form a hierarchy. As with the stem classification, both structural and functional groups exist. == See also == List of gene families Protein family == References ==
|
{
"page_id": 526719,
"source": null,
"title": "Gene family"
}
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A chemical equation is the symbolic representation of a chemical reaction in the form of symbols and chemical formulas. The reactant entities are given on the left-hand side and the product entities are on the right-hand side with a plus sign between the entities in both the reactants and the products, and an arrow that points towards the products to show the direction of the reaction. The chemical formulas may be symbolic, structural (pictorial diagrams), or intermixed. The coefficients next to the symbols and formulas of entities are the absolute values of the stoichiometric numbers. The first chemical equation was diagrammed by Jean Beguin in 1615. == Structure == A chemical equation (see an example below) consists of a list of reactants (the starting substances) on the left-hand side, an arrow symbol, and a list of products (substances formed in the chemical reaction) on the right-hand side. Each substance is specified by its chemical formula, optionally preceded by a number called stoichiometric coefficient. The coefficient specifies how many entities (e.g. molecules) of that substance are involved in the reaction on a molecular basis. If not written explicitly, the coefficient is equal to 1. Multiple substances on any side of the equation are separated from each other by a plus sign. As an example, the equation for the reaction of hydrochloric acid with sodium can be denoted: 2HCl + 2Na → 2NaCl + H2 Given the formulas are fairly simple, this equation could be read as "two H-C-L plus two N-A yields two N-A-C-L and H two." Alternately, and in general for equations involving complex chemicals, the chemical formulas are read using IUPAC nomenclature, which could verbalise this equation as "two hydrochloric acid molecules and two sodium atoms react to form two formula units of sodium chloride and a hydrogen gas
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molecule." === Reaction types === Different variants of the arrow symbol are used to denote the type of a reaction: === State of matter === To indicate physical state of a chemical, a symbol in parentheses may be appended to its formula: (s) for a solid, (l) for a liquid, (g) for a gas, and (aq) for an aqueous solution. This is especially done when one wishes to emphasize the states or changes thereof. For example, the reaction of aqueous hydrochloric acid with solid (metallic) sodium to form aqueous sodium chloride and hydrogen gas would be written like this: 2HCl(aq) + 2Na(s) → 2NaCl(aq) + H2(g) That reaction would have different thermodynamic and kinetic properties if gaseous hydrogen chloride were to replace the hydrochloric acid as a reactant: 2HCl(g) + 2Na(s) → 2NaCl(s) + H2(g) Alternately, an arrow without parentheses is used in some cases to indicate formation of a gas ↑ or precipitate ↓. This is especially useful if only one such species is formed. Here is an example indicating that hydrogen gas is formed: 2HCl + 2Na → 2 NaCl + H2 ↑ === Catalysis and other conditions === If the reaction requires energy, it is indicated above the arrow. A capital Greek letter delta (Δ) or a triangle (△) is put on the reaction arrow to show that energy in the form of heat is added to the reaction. The expression hν is used as a symbol for the addition of energy in the form of light. Other symbols are used for other specific types of energy or radiation. Similarly, if a reaction requires a certain medium with certain specific characteristics, then the name of the acid or base that is used as a medium may be placed on top of the arrow. If no specific acid
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or base is required, another way of denoting the use of an acidic or basic medium is to write H+ or OH− (or even "acid" or "base") on top of the arrow. Specific conditions of the temperature and pressure, as well as the presence of catalysts, may be indicated in the same way. === Notation variants === The standard notation for chemical equations only permits all reactants on one side, all products on the other, and all stoichiometric coefficients positive. For example, the usual form of the equation for dehydration of methanol to dimethylether is: 2 CH3OH → CH3OCH3 + H2O Sometimes an extension is used, where some substances with their stoichiometric coefficients are moved above or below the arrow, preceded by a plus sign or nothing for a reactant, and by a minus sign for a product. Then the same equation can look like this: 2 CH 3 OH → − H 2 O CH 3 OCH 3 {\displaystyle {\ce {2CH3OH->[{\overset {}{\ce {-H2O}}}]CH3OCH3}}} Such notation serves to hide less important substances from the sides of the equation, to make the type of reaction at hand more obvious, and to facilitate chaining of chemical equations. This is very useful in illustrating multi-step reaction mechanisms. Note that the substances above or below the arrows are not catalysts in this case, because they are consumed or produced in the reaction like ordinary reactants or products. Another extension used in reaction mechanisms moves some substances to branches of the arrow. Both extensions are used in the example illustration of a mechanism. Use of negative stoichiometric coefficients at either side of the equation (like in the example below) is not widely adopted and is often discouraged. 2 CH 3 OH − H 2 O ⟶ CH 3 OCH 3 {\displaystyle {\ce {2 CH3OH \;-\;
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H2O -> CH3OCH3}}} == Balancing chemical equations == Because no nuclear reactions take place in a chemical reaction, the chemical elements pass through the reaction unchanged. Thus, each side of the chemical equation must represent the same number of atoms of any particular element (or nuclide, if different isotopes are taken into account). The same holds for the total electric charge, as stated by the charge conservation law. An equation adhering to these requirements is said to be balanced. A chemical equation is balanced by assigning suitable values to the stoichiometric coefficients. Simple equations can be balanced by inspection, that is, by trial and error. Another technique involves solving a system of linear equations. Balanced equations are usually written with smallest natural-number coefficients. Yet sometimes it may be advantageous to accept a fractional coefficient, if it simplifies the other coefficients. The introductory example can thus be rewritten as HCl + Na ⟶ NaCl + 1 2 H 2 {\displaystyle {\ce {HCl + Na -> NaCl + 1/2 H2}}} In some circumstances the fractional coefficients are even inevitable. For example, the reaction corresponding to the standard enthalpy of formation must be written such that one molecule of a single product is formed. This will often require that some reactant coefficients be fractional, as is the case with the formation of lithium fluoride: Li ( s ) + 1 2 F 2 ( g ) ⟶ LiF ( s ) {\displaystyle {\ce {Li(s) + 1/2F2(g) -> LiF(s)}}} === Inspection method === The method of inspection can be outlined as setting the most complex substance's stoichiometric coefficient to 1 and assigning values to other coefficients step by step such that both sides of the equation end up with the same number of atoms for each element. If any fractional coefficients arise during this
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process, the presence of fractions may be eliminated (at any time) by multiplying all coefficients by their lowest common denominator. Example Balancing of the chemical equation for the complete combustion of methane ? CH 4 + ? O 2 ⟶ ? CO 2 + ? H 2 O {\displaystyle {\ce {{\mathord {?}}\,{CH4}+{\mathord {?}}\,{O2}->{\mathord {?}}\,{CO2}+{\mathord {?}}\,{H2O}}}} is achieved as follows: A coefficient of 1 is placed in front of the most complex formula (CH4): 1 CH 4 + ? O 2 ⟶ ? CO 2 + ? H 2 O {\displaystyle {\ce {1{CH4}+{\mathord {?}}\,{O2}->{\mathord {?}}\,{CO2}+{\mathord {?}}\,{H2O}}}} The left-hand side has 1 carbon atom, so 1 molecule of CO2 will balance it. The left-hand side also has 4 hydrogen atoms, which will be balanced by 2 molecules of H2O: 1 CH 4 + ? O 2 ⟶ 1 CO 2 + 2 H 2 O {\displaystyle {\ce {1{CH4}+{\mathord {?}}\,{O2}->1{CO2}+2H2O}}} Balancing the 4 oxygen atoms of the right-hand side by 2 molecules of O2 yields the equation 1 CH 4 + 2 O 2 ⟶ 1 CO 2 + 2 H 2 O {\displaystyle {\ce {1 CH4 + 2 O2 -> 1 CO2 + 2 H2O}}} The coefficients equal to 1 are omitted, as they do not need to be specified explicitly: CH 4 + 2 O 2 ⟶ CO 2 + 2 H 2 O {\displaystyle {\ce {CH4 + 2 O2 -> CO2 + 2 H2O}}} It is wise to check that the final equation is balanced, i.e. that for each element there is the same number of atoms on the left- and right-hand side: 1 carbon, 4 hydrogen, and 4 oxygen. === System of linear equations === For each chemical element (or nuclide or unchanged moiety or charge) i, its conservation requirement can be expressed by the mathematical equation ∑ j
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∈ reactants a i j s j = ∑ j ∈ products a i j s j {\displaystyle \sum _{j\,\in \,{\text{reactants}}}\!\!\!\!\!a_{ij}s_{j}\ =\!\!\!\!\!\sum _{j\,\in \,{\text{products}}}\!\!\!\!\!a_{ij}s_{j}} where aij is the number of atoms of element i in a molecule of substance j (per formula in the chemical equation), and sj is the stoichiometric coefficient for the substance j. This results in a homogeneous system of linear equations, which are readily solved using mathematical methods. Such system always has the all-zeros trivial solution, which we are not interested in, but if there are any additional solutions, there will be infinite number of them. Any non-trivial solution will balance the chemical equation. A "preferred" solution is one with whole-number, mostly positive stoichiometric coefficients sj with greatest common divisor equal to one. ==== Example ==== Let us assign variables to stoichiometric coefficients of the chemical equation from the previous section and write the corresponding linear equations: s 1 CH 4 + s 2 O 2 ⟶ s 3 CO 2 + s 4 H 2 O {\displaystyle {\ce {{\mathit {s}}_{1}{CH4}+{\mathit {s}}_{2}{O2}->{\mathit {s}}_{3}{CO2}+{\mathit {s}}_{4}{H2O}}}} C: s 1 = s 3 H: 4 s 1 = 2 s 4 O: 2 s 2 = 2 s 3 + s 4 {\displaystyle \quad \;\;\;{\begin{aligned}{\text{C:}}&&s_{1}&=s_{3}\\{\text{H:}}&&4s_{1}&=2s_{4}\\{\text{O:}}&&2s_{2}&=2s_{3}+s_{4}\end{aligned}}} All solutions to this system of linear equations are of the following form, where r is any real number: s 1 = r s 2 = 2 r s 3 = r s 4 = 2 r {\displaystyle {\begin{aligned}s_{1}&=r\\s_{2}&=2r\\s_{3}&=r\\s_{4}&=2r\end{aligned}}} The choice of r = 1 yields the preferred solution, s 1 = 1 s 2 = 2 s 3 = 1 s 4 = 2 {\displaystyle {\begin{aligned}s_{1}&=1\\s_{2}&=2\\s_{3}&=1\\s_{4}&=2\end{aligned}}} which corresponds to the balanced chemical equation: CH 4 + 2 O 2 ⟶ CO 2 + 2 H 2 O {\displaystyle {\ce {CH4 + 2 O2
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-> CO2 + 2 H2O}}} === Matrix method === The system of linear equations introduced in the previous section can also be written using an efficient matrix formalism. First, to unify the reactant and product stoichiometric coefficients sj, let us introduce the quantity ν j = { − s j for a reactant + s j for a product {\displaystyle \nu _{j}={\begin{cases}-s_{j}&{\text{for a reactant}}\\+s_{j}&{\text{for a product}}\end{cases}}} called stoichiometric number, which simplifies the linear equations to ∑ j = 1 J a i j ν j = 0 {\displaystyle \sum _{j=1}^{J}a_{ij}\nu _{j}=0} where J is the total number of reactant and product substances (formulas) in the chemical equation. Placement of the values aij at row i and column j of the composition matrix A = [ a 1 , 1 a 1 , 2 ⋯ a 1 , J a 2 , 1 a 2 , 2 ⋯ a 2 , J ⋮ ⋮ ⋱ ⋮ ] {\displaystyle {\begin{bmatrix}a_{1,1}&a_{1,2}&\cdots &a_{1,J}\\a_{2,1}&a_{2,2}&\cdots &a_{2,J}\\\vdots &\vdots &\ddots &\vdots \end{bmatrix}}} and arrangement of the stoichiometric numbers into the stoichiometric vector ν = [ ν 1 ν 2 ⋮ ν J ] {\displaystyle {\begin{bmatrix}\nu _{1}\\\nu _{2}\\\vdots \\\nu _{J}\end{bmatrix}}} allows the system of equations to be expressed as a single matrix equation: Aν = 0 Like previously, any nonzero stoichiometric vector ν, which solves the matrix equation, will balance the chemical equation. The set of solutions to the matrix equation is a linear space called the kernel of the matrix A. For this space to contain nonzero vectors ν, i.e. to have a positive dimension JN, the columns of the composition matrix A must not be linearly independent. The problem of balancing a chemical equation then becomes the problem of determining the JN-dimensional kernel of the composition matrix. It is important to note that only for JN =
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1 will there be a unique preferred solution to the balancing problem. For JN > 1 there will be an infinite number of preferred solutions with JN of them linearly independent. If JN = 0, there will be only the unusable trivial solution, the zero vector. Techniques have been developed to quickly calculate a set of JN independent solutions to the balancing problem, which are superior to the inspection and algebraic method in that they are determinative and yield all solutions to the balancing problem. Example Using the same chemical equation again, write the corresponding matrix equation: s 1 CH 4 + s 2 O 2 ⟶ s 3 CO 2 + s 4 H 2 O {\displaystyle {\ce {{\mathit {s}}_{1}{CH4}+{\mathit {s}}_{2}{O2}->{\mathit {s}}_{3}{CO2}+{\mathit {s}}_{4}{H2O}}}} C: H: O: [ 1 0 1 0 4 0 0 2 0 2 2 1 ] [ ν 1 ν 2 ν 3 ν 4 ] = 0 {\displaystyle {\begin{matrix}{\text{C:}}\\{\text{H:}}\\{\text{O:}}\end{matrix}}\quad {\begin{bmatrix}1&0&1&0\\4&0&0&2\\0&2&2&1\end{bmatrix}}{\begin{bmatrix}\nu _{1}\\\nu _{2}\\\nu _{3}\\\nu _{4}\end{bmatrix}}=\mathbf {0} } Its solutions are of the following form, where r is any real number: [ ν 1 ν 2 ν 3 ν 4 ] = [ − s 1 − s 2 s 3 s 4 ] = r [ − 1 − 2 1 2 ] {\displaystyle {\begin{bmatrix}\nu _{1}\\\nu _{2}\\\nu _{3}\\\nu _{4}\end{bmatrix}}={\begin{bmatrix}-s_{1}\\-s_{2}\\s_{3}\\s_{4}\end{bmatrix}}=r{\begin{bmatrix}-1\\-2\\1\\2\end{bmatrix}}} The choice of r = 1 and a sign-flip of the first two rows yields the preferred solution to the balancing problem: [ − ν 1 − ν 2 ν 3 ν 4 ] = [ s 1 s 2 s 3 s 4 ] = [ 1 2 1 2 ] {\displaystyle {\begin{bmatrix}-\nu _{1}\\-\nu _{2}\\\nu _{3}\\\nu _{4}\end{bmatrix}}={\begin{bmatrix}s_{1}\\s_{2}\\s_{3}\\s_{4}\end{bmatrix}}={\begin{bmatrix}1\\2\\1\\2\end{bmatrix}}} == Ionic equations == An ionic equation is a chemical equation in which electrolytes are written as dissociated ions. Ionic equations are used for single and double displacement
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"page_id": 199040,
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reactions that occur in aqueous solutions. For example, in the following precipitation reaction: CaCl 2 + 2 AgNO 3 ⟶ Ca ( NO 3 ) 2 + 2 AgCl ↓ {\displaystyle {\ce {CaCl2 + 2AgNO3 -> Ca(NO3)2 + 2 AgCl(v)}}} the full ionic equation is: Ca 2 + + 2 Cl − + 2 Ag + + 2 NO 3 − ⟶ Ca 2 + + 2 NO 3 − + 2 AgCl ↓ {\displaystyle {\ce {Ca^2+ + 2Cl^- + 2Ag+ + 2NO3^- -> Ca^2+ + 2NO3^- + 2AgCl(v)}}} or, with all physical states included: Ca 2 + ( aq ) + 2 Cl − ( aq ) + 2 Ag + ( aq ) + 2 NO 3 − ( aq ) ⟶ Ca 2 + ( aq ) + 2 NO 3 − ( aq ) + 2 AgCl ↓ {\displaystyle {\ce {Ca^2+(aq) + 2Cl^{-}(aq) + 2Ag+(aq) + 2NO3^{-}(aq) -> Ca^2+(aq) + 2NO3^{-}(aq) + 2AgCl(v)}}} In this reaction, the Ca2+ and the NO3− ions remain in solution and are not part of the reaction. That is, these ions are identical on both the reactant and product side of the chemical equation. Because such ions do not participate in the reaction, they are called spectator ions. A net ionic equation is the full ionic equation from which the spectator ions have been removed. The net ionic equation of the proceeding reactions is: 2 Cl − + 2 Ag + ⟶ 2 AgCl ↓ {\displaystyle {\ce {2Cl^- + 2Ag+ -> 2AgCl(v)}}} or, in reduced balanced form, Ag + + Cl − ⟶ AgCl ↓ {\displaystyle {\ce {Ag+ + Cl^- -> AgCl(v)}}} In a neutralization or acid/base reaction, the net ionic equation will usually be: H + ( aq ) + OH − ( aq ) ⟶ H 2 O (
|
{
"page_id": 199040,
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l ) {\displaystyle {\ce {H+ (aq) + OH^{-}(aq) -> H2O(l)}}} There are a few acid/base reactions that produce a precipitate in addition to the water molecule shown above. An example is the reaction of barium hydroxide with phosphoric acid, which produces not only water but also the insoluble salt barium phosphate. In this reaction, there are no spectator ions, so the net ionic equation is the same as the full ionic equation. 3 Ba ( OH ) 2 + 2 H 3 PO 4 ⟶ 6 H 2 O + Ba 3 ( PO 4 ) 2 ↓ {\displaystyle {\ce {3Ba(OH)2 + 2H3PO4 -> 6H2O + Ba3(PO4)2(v)}}} 3 Ba 2 + + 6 OH − + 6 H + + 2 PO 4 3 − ⏟ phosphate ⟶ 6 H 2 O + Ba 3 ( PO 4 ) 2 ↓ ⏟ barium phosphate {\displaystyle {\ce {{3Ba^{2}+}+{6OH^{-}}+{6H+}}}+\underbrace {\ce {2PO4^{3}-}} _{\ce {phosphate}}{\ce {->{6H2O}+\underbrace {Ba3(PO4)2(v)} _{barium~phosphate}}}} Double displacement reactions that feature a carbonate reacting with an acid have the net ionic equation: 2 H + + CO 3 2 − ⏟ carbonate ⟶ H 2 O + CO 2 ↑ {\displaystyle {\ce {2H+}}+\underbrace {{\ce {CO3^2-}}} _{{\ce {carbonate}}}{\ce {-> H2O + CO2 (^)}}} If every ion is a "spectator ion" then there was no reaction, and the net ionic equation is null. Generally, if zj is the multiple of elementary charge on the j-th molecule, charge neutrality may be written as: ∑ j = 1 J z j ν j = 0 {\displaystyle \sum _{j=1}^{J}z_{j}\nu _{j}=0} where the νj are the stoichiometric coefficients described above. The zj may be incorporated as an additional row in the aij matrix described above, and a properly balanced ionic equation will then also obey: ∑ j = 1 J a i j ν j = 0 {\displaystyle
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\sum _{j=1}^{J}a_{ij}\nu _{j}=0} == History == == Typesetting == == See also == Mathematical notation Comparison of TeX editors TeX extentions for science and chemistry notation Chemistry notation in TeX == Notes == == References ==
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{
"page_id": 199040,
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Homopolysaccharides are polysaccharides composed of a single type of sugar monomer. For example, cellulose is an unbranched homopolysaccharide made up of glucose monomers connected via beta-glycosidic linkages; glycogen is a branched form, where the glucose monomers are joined by alpha-glycosidic linkages. Depending upon the molecules attached that are of the following types: Glucan - A polysaccharide of glucose Fructan - A polysaccharide of fructose Galactan - A polysaccharide of galactose Arabinan - A polysaccharide of arabinose Xylan - A polysaccharide of xylose == References ==
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{
"page_id": 15206784,
"source": null,
"title": "Homopolysaccharide"
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The peroxide process is a method for the industrial production of hydrazine. In this process hydrogen peroxide is used as an oxidant instead of sodium hypochlorite, which is traditionally used to generate hydrazine. The main advantage of the peroxide process to hydrazine relative to the traditional Olin Raschig process is that it does not coproduce salt. In this respect, the peroxide process is an example of green chemistry. Since many millions of kilograms of hydrazine are produced annually, this method is of both commercial and environmental significance. == Production == === Ketazine formation === In the usual implementation, hydrogen peroxide is used together with acetamide. This mixture does not react with ammonia directly but does so in the presence of methyl ethyl ketone to give the oxaziridine. Balanced equations for the individual steps are as follows. Imine formation through condensation: Me(Et)C=O + NH3 → Me(Et)C=NH + H2O Oxidation of the imine to the oxaziridine: Me(Et)C=NH + H2O2 → Me(Et)CONH + H2O Condensation of the oxaziridine with a second molecule of ammonia to give the hydrazone: Me(Et)CONH + NH3 → Me(Et)C=NNH2 + H2O The hydrazone then condenses with a second equivalent of ketone to give the ketazine: Me(Et)C=O + Me(Et)C=NNH2 → Me(Et)C=NN=C(Et)Me + H2O Typical process conditions are 50 °C and atmospheric pressure, with a feed mix of H2O2:ketone:NH3 in a molar ratio of about 1:2:4. Methyl ethyl ketone is advantageous to acetone because the resulting ketazine is immiscible in the reaction mixture and can be separated by decantation. A similar process based on benzophenone has also been described. === Ketazine to hydrazine === The final stage involves hydrolysis of the purified ketazine: Me(Et)C=NN=C(Et)Me + 2 H2O → 2 Me(Et)C=O + N2H4 The hydrolysis of the azine is acid-catalyzed, hence the need to isolate the azine from the initial ammonia-containing reaction
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{
"page_id": 1116547,
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mixture. It is also endothermic, and so requires an increase in temperature (and pressure) to shift the equilibrium in favour of the desired products: ketone (which is recycled) and hydrazine hydrate. The reaction is carried out by simple distillation of the azeotrope: typical conditions are a pressure of 8 bar and temperatures of 130 °C at the top of the column and 179 °C at the bottom of the column. The hydrazine hydrate (30–45% aqueous solution) is run off from the base of the column, while the methyl ethyl ketone is distilled off from the top of the column and recycled. == History == The peroxide process, also called the Pechiney–Ugine–Kuhlmann process, was developed in the early 1970s by Produits Chimiques Ugine Kuhlmann. Originally the process used acetone instead of methyl ethyl ketone. Methyl ethyl ketone is advantageous because the resulting ketazine is immiscible in the reaction mixture and can be separated by decantation. The world's largest hydrazine hydrate plant is in Lannemezan in France, producing 17,000 tonnes of hydrazine products per year. === Bayer ketazine process === Before invention of the peroxide process, the Bayer ketazine process had been commercialized. In the Bayer process, the oxidation of ammonia by sodium hypochlorite is conducted in the presence of acetone. The process generates the ketazine but also sodium chloride: 2 Me2CO + 2 NH3 + NaOCl → Me2C=NN=CMe2 + 3 H2O + NaCl Me2C=NN=CMe2 + 2 H2O → N2H4 + 2 Me2CO == References ==
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{
"page_id": 1116547,
"source": null,
"title": "Peroxide process"
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The Fritsch–Buttenberg–Wiechell rearrangement, named for Paul Ernst Moritz Fritsch (1859–1913), Wilhelm Paul Buttenberg, and Heinrich G. Wiechell, is a chemical reaction whereby a 1,1-diaryl-2-bromo-alkene rearranges to a 1,2-diaryl-alkyne by reaction with a strong base such as an alkoxide. This rearrangement is also possible with alkyl substituents. == Reaction mechanism == The strong base deprotonates the vinylic hydrogen, which after alpha elimination forms a vinyl carbene. A 1,2-aryl migration forms the 1,2-diaryl-alkyne product. The mechanism of the FBW rearrangement was a subject of on-surface studies where the vinyl radical was visualised with sub-atomic resolution. == Scope == One study explored this reaction for the synthesis of novel polyynes: == See also == Corey–Fuchs reaction == References == Darses, B.; Milet, A.; Philouze, C.; Greene, A. E.; Poisson, J.-F. o., Ynol Ethers from Dichloroenol Ethers: Mechanistic Elucidation Through 35Cl Labeling. Organic Letters 2008, 10 (20), 4445-4447.
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{
"page_id": 2034059,
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"title": "Fritsch–Buttenberg–Wiechell rearrangement"
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In biological classification, circumscriptional names (Latin: nomina circumscribentia) are taxon names that are defined by their circumscription; i.e. the diagnostic feature of the particular set of members included. Such names are not ruled by any nomenclature code and are mainly for taxa above the rank of family (e.g. order or class), but can be used for taxa of any rank or unranked taxa. Non-typified names other than those of genus or species rank constitute the majority of generally accepted names of taxa higher than superfamily. The standard nomenclature codes regulate names of taxa up to family rank (i.e. superfamily). There are no generally accepted rules for the naming of higher taxa (orders, classes, phyla, etc.). Under the approach of circumscription-based (circumscriptional) nomenclatures, a circumscriptional name is associated with a certain circumscription of a taxon without regard of its rank or position. In contrast to circumscriptional nomenclature, some authors advocate introducing a mandatory standardized typified nomenclature of higher taxa. They suggest all names of higher taxa to be derived in the same manner as family-group names, by modifying names of type genera with suffixes to reflect the rank. There is no consensus on what such higher rank suffixes should be. A number of established practices exist as to the use of typified names of higher taxa, depending on group of organisms. == See also == Descriptive botanical name, optional forms still used in botany for ranks above family and for a few family names == References == Kluge, N. 2000. "Sovremennaya Sistematika Nasekomyh ..." [Modern Systematics of Insects. Part I. Principles of Systematics of Living Organisms and General System of Insects, with Classification of Primary Wingless and Paleopterous Insects] - S.-Petersburg, Lan', 2000, 333 pp.; (c) N.Ju. Kluge, 2000; (c) "Lan'", 2000. Kluge N.J. 2010. Circumscriptional names of higher taxa in
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{
"page_id": 4721036,
"source": null,
"title": "Circumscriptional name"
}
|
Hexapoda. // Bionomina, 1: 15–55. https://www.mapress.com/bionomina/content/2010/f/bn00001p055.pdf == External links == Kluge's PRINCIPLES OF NOMENCLATURE of ZOOLOGICAL TAXA NOMINA CIRCUMSCRIBENTIA INSECTORUM
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"page_id": 4721036,
"source": null,
"title": "Circumscriptional name"
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Palladium(II) bis(acetylacetonate) is a compound with formula Pd(C5H7O2)2. This yellow solid is the most common palladium complex of acetylacetonate. This compound is commercially available and used as a catalyst precursor in organic synthesis. The molecule is relatively planar with idealized D2h symmetry. == See also == Platinum(II) bis(acetylacetonate) Nickel(II) bis(acetylacetonate) == References ==
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{
"page_id": 10815888,
"source": null,
"title": "Palladium(II) bis(acetylacetonate)"
}
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Sabouraud agar or Sabouraud dextrose agar (SDA) is a type of agar growth medium containing peptones. It is used to cultivate dermatophytes and other types of fungi, and can also grow filamentous bacteria such as Nocardia. It has utility for research and clinical care. It was created by, and is named after, Raymond Sabouraud in 1892. In 1977 the formulation was adjusted by Chester W. Emmons when the pH level was brought closer to the neutral range and the dextrose concentration lowered to support the growth of other microorganisms. The acidic pH (5.6) of traditional Sabouraud agar inhibits bacterial growth. Peptones are complex digests and can be a source of variability in Sabouraud agar. == Typical composition == Sabouraud agar is commercially available and typically contains: 40 g/L dextrose 10 g/L peptone 20 g/L agar pH 5.6 == Medical use == Clinical laboratories can use this growth medium to diagnose and further speciate fungal infections, allowing medical professionals to provide appropriate treatment with antifungal medications. Histoplasma and other fungal causes of atypical pneumonia can be grown on this medium. Sabouraud agar used in combination with additional media, such as Inhibitory Mold Agar (IMA), improves identification of fungal clinical isolates. == References ==
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{
"page_id": 19925395,
"source": null,
"title": "Sabouraud agar"
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Cryomyces minteri is a fungus of uncertain placement in the class Dothideomycetes, division Ascomycota. The rock-inhabiting fungus that was discovered in the McMurdo Dry Valleys located in Antarctica, on fragments of rock colonized by a local cryptoendolithic community. In 2008, Cryomyces minteri and Cryomyces antarcticus were simultaneously tested in low Earth orbit conditions on the EXPOSE-E facility on the EuTEF (European Technology Exposure Facility) platform outside the International Space Station for 18 months. It was also tested in a space vacuum along with polychromatic UV radiation to simulate a Martian environment. The two fungi survived both of the simulations. == References == == External links == Catalogue of Life: Dothideomycetes
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"page_id": 51775892,
"source": null,
"title": "Cryomyces minteri"
}
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In biochemistry, intercalation is the insertion of molecules between the planar bases of deoxyribonucleic acid (DNA). This process is used as a method for analyzing DNA and it is also the basis of certain kinds of poisoning. There are several ways molecules (in this case, also known as ligands) can interact with DNA. Ligands may interact with DNA by covalently binding, electrostatically binding, or intercalating. Intercalation occurs when ligands of an appropriate size and chemical nature fit themselves in between base pairs of DNA. These ligands are mostly polycyclic, aromatic, and planar, and therefore often make good nucleic acid stains. Intensively studied DNA intercalators include berberine, ethidium bromide, proflavine, daunomycin, doxorubicin, and thalidomide. DNA intercalators are used in chemotherapeutic treatment to inhibit DNA replication in rapidly growing cancer cells. Examples include doxorubicin (adriamycin) and daunorubicin (both of which are used in treatment of Hodgkin's lymphoma), and dactinomycin (used in Wilm's tumour, Ewing's Sarcoma, rhabdomyosarcoma). Metallointercalators are complexes of a metal cation with polycyclic aromatic ligands. The most commonly used metal ion is ruthenium(II), because its complexes are very slow to decompose in the biological environment. Other metallic cations that have been used include rhodium(III) and iridium(III). Typical ligands attached to the metal ion are dipyridine and terpyridine whose planar structure is ideal for intercalation. In order for an intercalator to fit between base pairs, the DNA must dynamically open a space between its base pairs by unwinding. The degree of unwinding varies depending on the intercalator; for example, ethidium cation (the ionic form of ethidium bromide found in aqueous solution) unwinds DNA by about 26°, whereas proflavine unwinds it by about 17°. This unwinding causes the base pairs to separate, or "rise", creating an opening of about 0.34 nm (3.4 Å). Similarly, in the case of the intercalation of Thiazole
|
{
"page_id": 42600851,
"source": null,
"title": "Intercalation (biochemistry)"
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Orange derivatives, the distance between the base pairs increased significantly, from ca. 4.7 Å to ca, 6.9. This unwinding induces local structural changes to the DNA strand, such as lengthening of the DNA strand or twisting of the base pairs. These structural modifications can lead to functional changes, often to the inhibition of transcription and replication and DNA repair processes, which makes intercalators potent mutagens. For this reason, DNA intercalators are often carcinogenic, such as the exo (but not the endo) 8,9 epoxide of aflatoxin B1 and acridines such as proflavine or quinacrine. Intercalation as a mechanism of interaction between cationic, planar, polycyclic aromatic systems of the correct size (on the order of a base pair) was first proposed by Leonard Lerman in 1961. One proposed mechanism of intercalation is as follows: In aqueous isotonic solution, the cationic intercalator is attracted electrostatically to the surface of the polyanionic DNA. The ligand displaces a sodium and/or magnesium cation present in the "condensation cloud" of such cations that surrounds DNA (to partially balance the sum of the negative charges carried by each phosphate oxygen), thus forming a weak electrostatic association with the outer surface of DNA. From this position, the ligand diffuses along the surface of the DNA and may slide into the hydrophobic environment found between two base pairs that may transiently "open" to form an intercalation site, allowing the ethidium to move away from the hydrophilic (aqueous) environment surrounding the DNA and into the intercalation site. The base pairs transiently form such openings due to energy absorbed during collisions with solvent molecules. == See also == Anthracycline Intercalation (chemistry) Molecular tweezers Twisted intercalating nucleic acid == References ==
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{
"page_id": 42600851,
"source": null,
"title": "Intercalation (biochemistry)"
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This is a list of investigational anxiolytics, or anxiolytics that are currently under development for clinical use but are not yet approved. Chemical/generic names are listed first, with developmental code names, synonyms, and brand names in parentheses. This list was last comprehensively updated in June 2017. It is likely to become outdated with time. == Generalized anxiety disorder == Riluzole sublingual (BHV-0223) – undefined mechanism of action SPT-320 (LYT-320) – agomelatine prodrug (melatonin receptor agonist and serotonin 5-HT2B and 5-HT2C receptor antagonist) TGFK08AA – 5-HT1A receptor modulator TGW00AA (FKW00GA) – 5-HT1A receptor agonist, 5-HT2A receptor antagonist == Panic disorder == Darigabat (PF-06372865) – GABAA receptor positive allosteric modulator Tebideutorexant (JNJ-61393215, JNJ-3215) – orexin OX1 receptor antagonist == Post-traumatic stress disorder == 7-Oxoprasterone (7-keto-DHEA; HBL-9001) – "immunomodulator" / undefined mechanism of action Brexpiprazole (Lu AF41156, OPC-34712; Rexulti) – atypical antipsychotic / 5-HT1A, D2 and D3 receptor partial agonist and 5-HT2A, 5-HT2B, 5-HT7, α1-adrenergic, α2-adrenergic, and H1 receptor antagonist Iloperidone (HP-873, ILO-522; Fanapt, Fiapta, Zomaril) – atypical antipsychotic / 5-HT2A, 5-HT6, 5-HT7, D2, D3, D4, and α1-adrenergic receptor antagonist MDMA (Midomafetamine, 3,4-methylenedioxymethamphetamine, "ecstasy") – serotonin–norepinephrine–dopamine releasing agent and 5-HT1 and 5-HT2 receptor agonist – specifically under development as an aid to psychotherapy for post-traumatic stress disorder NBTX-001 (Xenon) – NMDA receptor antagonist Pomaglumetad methionil (DB-103, LY-2140023) – mGluR2 and mGluR3 agonist Soclenicant (BNC-210; IW-2143) – "GABATooltip γ-aminobutyric acid modulator" / undefined mechanism of action Tianeptine oxalate/naloxone (TNX-601) – atypical μ-opioid receptor agonist == Social anxiety disorder == Fasedienol (Aloradine; PH94B; 4-androstadienol) – vomeropherine / neurosteroid JNJ-42165279 – FAAH inhibitor TGW00AA (FKW00GA) – 5-HT1A receptor agonist, 5-HT2A receptor antagonist == Others/unspecified == Brexanolone caprilcerbate (LYT-300, SPT-300) – orally active brexanolone (allopregnanolone) prodrug and GABAA receptor positive allosteric modulator Deuterated etifoxine (GRX-917) – translocator protein (TSPO) agonist and GABAA receptor positive allosteric modulator JNJ-42165279
|
{
"page_id": 54200726,
"source": null,
"title": "List of investigational anxiolytics"
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– FAAH inhibitor JNJ-61393215 – orexin OX1 receptor antagonist Maritupirdine (AVN-101; Aviandr) – 5-HT6 receptor antagonist MP-20X – CB1 and 5-HT1A receptor modulator Soclenicant (BNC-210; IW-2143) – "GABA modulator" / undefined mechanism of action / α7 subunit-containing nicotinic acetylcholine receptor antagonist SRX-246 – vasopressin V1A receptor antagonist Trideca-7,9,11-trienoic_acid - pharmacological mechanism of action unknown == See also == List of investigational drugs List of investigational social anxiety disorder drugs == References == == External links == AdisInsight – Springer 2016 Medicines in Development for Mental Health - PhRMA
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{
"page_id": 54200726,
"source": null,
"title": "List of investigational anxiolytics"
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Dithiole is a type of sulfur-containing heterocycle. The parent members have the formula C3H4S2. Dithioles exist in two isomers: 1,2-Dithiole 1,3-Dithiole
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{
"page_id": 43911576,
"source": null,
"title": "Dithiole"
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Apoptosis (from Ancient Greek: ἀπόπτωσις, romanized: apóptōsis, lit. 'falling off') is a form of programmed cell death that occurs in multicellular organisms and in some eukaryotic, single-celled microorganisms such as yeast. Biochemical events lead to characteristic cell changes (morphology) and death. These changes include blebbing, cell shrinkage, nuclear fragmentation, chromatin condensation, DNA fragmentation, and mRNA decay. The average adult human loses 50 to 70 billion cells each day due to apoptosis. For the average human child between 8 and 14 years old, each day the approximate loss is 20 to 30 billion cells. In contrast to necrosis, which is a form of traumatic cell death that results from acute cellular injury, apoptosis is a highly regulated and controlled process that confers advantages during an organism's life cycle. For example, the separation of fingers and toes in a developing human embryo occurs because cells between the digits undergo a form of apoptosis that is genetically determined. Unlike necrosis, apoptosis produces cell fragments called apoptotic bodies that phagocytes are able to engulf and remove before the contents of the cell can spill out onto surrounding cells and cause damage to them. Because apoptosis cannot stop once it has begun, it is a highly regulated process. Apoptosis can be initiated through one of two pathways. In the intrinsic pathway the cell kills itself because it senses cell stress, while in the extrinsic pathway the cell kills itself because of signals from other cells. Weak external signals may also activate the intrinsic pathway of apoptosis. Both pathways induce cell death by activating caspases, which are proteases, or enzymes that degrade proteins. The two pathways both activate initiator caspases, which then activate executioner caspases, which then kill the cell by degrading proteins indiscriminately. In addition to its importance as a biological phenomenon, defective apoptotic processes
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{
"page_id": 2457,
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"title": "Apoptosis"
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have been implicated in a wide variety of diseases. Excessive apoptosis causes atrophy, whereas an insufficient amount results in uncontrolled cell proliferation, such as cancer. Some factors like Fas receptors and caspases promote apoptosis, while some members of the Bcl-2 family of proteins inhibit apoptosis. == Discovery and etymology == German scientist Carl Vogt was first to describe the principle of apoptosis in 1842. In 1885, anatomist Walther Flemming delivered a more precise description of the process of programmed cell death. However, it was not until 1965 that the topic was resurrected. While studying tissues using electron microscopy, John Kerr at the University of Queensland was able to distinguish apoptosis from traumatic cell death. Following the publication of a paper describing the phenomenon, Kerr was invited to join Alastair Currie, as well as Andrew Wyllie, who was Currie's graduate student, at the University of Aberdeen. In 1972, the trio published a seminal article in the British Journal of Cancer. Kerr had initially used the term programmed cell necrosis, but in the article, the process of natural cell death was called apoptosis. Kerr, Wyllie and Currie credited James Cormack, a professor of Greek language at University of Aberdeen, with suggesting the term apoptosis. Kerr received the Paul Ehrlich and Ludwig Darmstaedter Prize on March 14, 2000, for his description of apoptosis. He shared the prize with Boston biologist H. Robert Horvitz. For many years, neither "apoptosis" nor "programmed cell death" was a highly cited term. Two discoveries brought cell death from obscurity to a major field of research: identification of the first component of the cell death control and effector mechanisms, and linkage of abnormalities in cell death to human disease, in particular cancer. This occurred in 1988 when it was shown that BCL2, the gene responsible for follicular lymphoma, encoded
|
{
"page_id": 2457,
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"title": "Apoptosis"
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a protein that inhibited cell death. The 2002 Nobel Prize in Medicine was awarded to Sydney Brenner, H. Robert Horvitz and John Sulston for their work identifying genes that control apoptosis. The genes were identified by studies in the nematode C. elegans and homologues of these genes function in humans to regulate apoptosis. In Greek, apoptosis translates to the "falling off" of leaves from a tree. Cormack, professor of Greek language, reintroduced the term for medical use as it had a medical meaning for the Greeks over two thousand years before. Hippocrates used the term to mean "the falling off of the bones". Galen extended its meaning to "the dropping of the scabs". Cormack was no doubt aware of this usage when he suggested the name. Debate continues over the correct pronunciation, with opinion divided between a pronunciation with the second p silent ( ap-ə-TOH-sis) and the second p pronounced ( ). In English, the p of the Greek -pt- consonant cluster is typically silent at the beginning of a word (e.g. pterodactyl, Ptolemy), but articulated when used in combining forms preceded by a vowel, as in helicopter or the orders of insects: diptera, lepidoptera, etc. In the original Kerr, Wyllie & Currie paper, there is a footnote regarding the pronunciation: We are most grateful to Professor James Cormack of the Department of Greek, University of Aberdeen, for suggesting this term. The word "apoptosis" (ἀπόπτωσις) is used in Greek to describe the "dropping off" or "falling off" of petals from flowers, or leaves from trees. To show the derivation clearly, we propose that the stress should be on the penultimate syllable, the second half of the word being pronounced like "ptosis" (with the "p" silent), which comes from the same root "to fall", and is already used to describe the
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{
"page_id": 2457,
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drooping of the upper eyelid. == Activation mechanisms == The initiation of apoptosis is tightly regulated by activation mechanisms, because once apoptosis has begun, it inevitably leads to the death of the cell. The two best-understood activation mechanisms are the intrinsic pathway (also called the mitochondrial pathway) and the extrinsic pathway. The intrinsic pathway is activated by intracellular signals generated when cells are stressed and depends on the release of proteins from the intermembrane space of mitochondria. The extrinsic pathway is activated by extracellular ligands binding to cell-surface death receptors, which leads to the formation of the death-inducing signaling complex (DISC). A cell initiates intracellular apoptotic signaling in response to a stress, which may bring about cell death. The binding of nuclear receptors by glucocorticoids, heat, radiation, nutrient deprivation, viral infection, hypoxia, increased intracellular concentration of free fatty acids and increased intracellular calcium concentration, for example, by damage to the membrane, can all trigger the release of intracellular apoptotic signals by a damaged cell. A number of cellular components, such as poly ADP ribose polymerase, may also help regulate apoptosis. Single cell fluctuations have been observed in experimental studies of stress induced apoptosis. Before the actual process of cell death is precipitated by enzymes, apoptotic signals must cause regulatory proteins to initiate the apoptosis pathway. This step allows those signals to cause cell death, or the process to be stopped, should the cell no longer need to die. Several proteins are involved, but two main methods of regulation have been identified: the targeting of mitochondria functionality, or directly transducing the signal via adaptor proteins to the apoptotic mechanisms. An extrinsic pathway for initiation identified in several toxin studies is an increase in calcium concentration within a cell caused by drug activity, which also can cause apoptosis via a calcium binding
|
{
"page_id": 2457,
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protease calpain. === Intrinsic pathway === The intrinsic pathway is also known as the mitochondrial pathway. Mitochondria are essential to multicellular life. Without them, a cell ceases to respire aerobically and quickly dies. This fact forms the basis for some apoptotic pathways. Apoptotic proteins that target mitochondria affect them in different ways. They may cause mitochondrial swelling through the formation of membrane pores, or they may increase the permeability of the mitochondrial membrane and cause apoptotic effectors to leak out. There is also a growing body of evidence indicating that nitric oxide is able to induce apoptosis by helping to dissipate the membrane potential of mitochondria and therefore make it more permeable. Nitric oxide has been implicated in initiating and inhibiting apoptosis through its possible action as a signal molecule of subsequent pathways that activate apoptosis. During apoptosis, cytochrome c is released from mitochondria through the actions of the proteins Bax and Bak. The mechanism of this release is enigmatic, but appears to stem from a multitude of Bax/Bak homo- and hetero-dimers of Bax/Bak inserted into the outer membrane. Once cytochrome c is released it binds with Apoptotic protease activating factor – 1 (Apaf-1) and ATP, which then bind to pro-caspase-9 to create a protein complex known as an apoptosome. The apoptosome cleaves the pro-caspase to its active form of caspase-9, which in turn cleaves and activates pro-caspase into the effector caspase-3. Mitochondria also release proteins known as SMACs (second mitochondria-derived activator of caspases) into the cell's cytosol following the increase in permeability of the mitochondria membranes. SMAC binds to proteins that inhibit apoptosis (IAPs) thereby deactivating them, and preventing the IAPs from arresting the process and therefore allowing apoptosis to proceed. IAP also normally suppresses the activity of a group of cysteine proteases called caspases, which carry out the
|
{
"page_id": 2457,
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"title": "Apoptosis"
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degradation of the cell. Therefore, the actual degradation enzymes can be seen to be indirectly regulated by mitochondrial permeability. === Extrinsic pathway === Two theories of the direct initiation of apoptotic mechanisms in mammals have been suggested: the TNF-induced (tumor necrosis factor) model and the Fas-Fas ligand-mediated model, both involving receptors of the TNF receptor (TNFR) family coupled to extrinsic signals. ==== TNF pathway ==== TNF-alpha is a cytokine produced mainly by activated macrophages, and is the major extrinsic mediator of apoptosis. Most cells in the human body have two receptors for TNF-alpha: TNFR1 and TNFR2. The binding of TNF-alpha to TNFR1 has been shown to initiate the pathway that leads to caspase activation via the intermediate membrane proteins TNF receptor-associated death domain (TRADD) and Fas-associated death domain protein (FADD). cIAP1/2 can inhibit TNF-α signaling by binding to TRAF2. FLIP inhibits the activation of caspase-8. Binding of this receptor can also indirectly lead to the activation of transcription factors involved in cell survival and inflammatory responses. However, signalling through TNFR1 might also induce apoptosis in a caspase-independent manner. The link between TNF-alpha and apoptosis shows why an abnormal production of TNF-alpha plays a fundamental role in several human diseases, especially in autoimmune diseases. The TNF-alpha receptor superfamily also includes death receptors (DRs), such as DR4 and DR5. These receptors bind to the protein TRAIL and mediate apoptosis. Apoptosis is known to be one of the primary mechanisms of targeted cancer therapy. Luminescent iridium complex-peptide hybrids (IPHs) have recently been designed, which mimic TRAIL and bind to death receptors on cancer cells, thereby inducing their apoptosis. ==== Fas pathway ==== The fas receptor (First apoptosis signal) – (also known as Apo-1 or CD95) is a transmembrane protein of the TNF family which binds the Fas ligand (FasL). The interaction between Fas
|
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"page_id": 2457,
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and FasL results in the formation of the death-inducing signaling complex (DISC), which contains the FADD, caspase-8 and caspase-10. In some types of cells (type I), processed caspase-8 directly activates other members of the caspase family, and triggers the execution of apoptosis of the cell. In other types of cells (type II), the Fas-DISC starts a feedback loop that spirals into increasing release of proapoptotic factors from mitochondria and the amplified activation of caspase-8. ==== Common components ==== Following TNF-R1 and Fas activation in mammalian cells a balance between proapoptotic (BAX, BID, BAK, or BAD) and anti-apoptotic (Bcl-Xl and Bcl-2) members of the Bcl-2 family are established. This balance is the proportion of proapoptotic homodimers that form in the outer-membrane of the mitochondrion. The proapoptotic homodimers are required to make the mitochondrial membrane permeable for the release of caspase activators such as cytochrome c and SMAC. Control of proapoptotic proteins under normal cell conditions of nonapoptotic cells is incompletely understood, but in general, Bax or Bak are activated by the activation of BH3-only proteins, part of the Bcl-2 family. ==== Caspases ==== Caspases play the central role in the transduction of ER apoptotic signals. Caspases are proteins that are highly conserved, cysteine-dependent aspartate-specific proteases. There are two types of caspases: initiator caspases (caspases 2, 8, 9, 10, 11, and 12) and effector caspases (caspases 3, 6, and 7). The activation of initiator caspases requires binding to specific oligomeric activator protein. Effector caspases are then activated by these active initiator caspases through proteolytic cleavage. The active effector caspases then proteolytically degrade a host of intracellular proteins to carry out the cell death program. ==== Caspase-independent apoptotic pathway ==== There also exists a caspase-independent apoptotic pathway that is mediated by AIF (apoptosis-inducing factor). === Apoptosis model in amphibians === The frog Xenopus
|
{
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"title": "Apoptosis"
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laevis serves as an ideal model system for the study of the mechanisms of apoptosis. In fact, iodine and thyroxine also stimulate the spectacular apoptosis of the cells of the larval gills, tail and fins in amphibian's metamorphosis, and stimulate the evolution of their nervous system transforming the aquatic, vegetarian tadpole into the terrestrial, carnivorous frog. == Negative regulators of apoptosis == Negative regulation of apoptosis inhibits cell death signaling pathways, helping tumors to evade cell death and developing drug resistance. The ratio between anti-apoptotic (Bcl-2) and pro-apoptotic (Bax) proteins determines whether a cell lives or dies. Many families of proteins act as negative regulators categorized into either antiapoptotic factors, such as IAPs and Bcl-2 proteins or prosurvival factors like cFLIP, BNIP3, FADD, Akt, and NF-κB. == Proteolytic caspase cascade: Killing the cell == Many pathways and signals lead to apoptosis, but these converge on a single mechanism that actually causes the death of the cell. After a cell receives stimulus, it undergoes organized degradation of cellular organelles by activated proteolytic caspases. In addition to the destruction of cellular organelles, mRNA is rapidly and globally degraded by a mechanism that is not yet fully characterized. mRNA decay is triggered very early in apoptosis. A cell undergoing apoptosis shows a series of characteristic morphological changes. Early alterations include: Cell shrinkage and rounding occur because of the retraction of lamellipodia and the breakdown of the proteinaceous cytoskeleton by caspases. The cytoplasm appears dense, and the organelles appear tightly packed. Chromatin undergoes condensation into compact patches against the nuclear envelope (also known as the perinuclear envelope) in a process known as pyknosis, a hallmark of apoptosis. The nuclear envelope becomes discontinuous and the DNA inside it is fragmented in a process referred to as karyorrhexis. The nucleus breaks into several discrete chromatin bodies
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{
"page_id": 2457,
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"title": "Apoptosis"
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or nucleosomal units due to the degradation of DNA. Apoptosis progresses quickly and its products are quickly removed, making it difficult to detect or visualize on classical histology sections. During karyorrhexis, endonuclease activation leaves short DNA fragments, regularly spaced in size. These give a characteristic "laddered" appearance on agar gel after electrophoresis. Tests for DNA laddering differentiate apoptosis from ischemic or toxic cell death. === Apoptotic cell disassembly === Before the apoptotic cell is disposed of, there is a process of disassembly. There are three recognized steps in apoptotic cell disassembly: Membrane blebbing: The cell membrane shows irregular buds known as blebs. Initially these are smaller surface blebs. Later these can grow into larger so-called dynamic membrane blebs. An important regulator of apoptotic cell membrane blebbing is ROCK1 (rho associated coiled-coil-containing protein kinase 1). Formation of membrane protrusions: Some cell types, under specific conditions, may develop different types of long, thin extensions of the cell membrane called membrane protrusions. Three types have been described: microtubule spikes, apoptopodia (feet of death), and beaded apoptopodia (the latter having a beads-on-a-string appearance). Pannexin 1 is an important component of membrane channels involved in the formation of apoptopodia and beaded apoptopodia. Fragmentation: The cell breaks apart into multiple vesicles called apoptotic bodies, which undergo phagocytosis. The plasma membrane protrusions may help bring apoptotic bodies closer to phagocytes. === Removal of dead cells === The removal of dead cells by neighboring phagocytic cells has been termed efferocytosis. Dying cells that undergo the final stages of apoptosis display phagocytotic molecules, such as phosphatidylserine, on their cell surface. Phosphatidylserine is normally found on the inner leaflet surface of the plasma membrane, but is redistributed during apoptosis to the extracellular surface by a protein known as scramblase. These molecules mark the cell for phagocytosis by cells possessing the
|
{
"page_id": 2457,
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appropriate receptors, such as macrophages. The removal of dying cells by phagocytes occurs in an orderly manner without eliciting an inflammatory response. During apoptosis cellular RNA and DNA are separated from each other and sorted to different apoptotic bodies; separation of RNA is initiated as nucleolar segregation. == Pathway knock-outs == Many knock-outs have been made in the apoptosis pathways to test the function of each of the proteins. Several caspases, in addition to APAF1 and FADD, have been mutated to determine the new phenotype. In order to create a tumor necrosis factor (TNF) knockout, an exon containing the nucleotides 3704–5364 was removed from the gene. This exon encodes a portion of the mature TNF domain, as well as the leader sequence, which is a highly conserved region necessary for proper intracellular processing. TNF-/- mice develop normally and have no gross structural or morphological abnormalities. However, upon immunization with SRBC (sheep red blood cells), these mice demonstrated a deficiency in the maturation of an antibody response; they were able to generate normal levels of IgM, but could not develop specific IgG levels. Apaf-1 is the protein that turns on caspase 9 by cleavage to begin the caspase cascade that leads to apoptosis. Since a -/- mutation in the APAF-1 gene is embryonic lethal, a gene trap strategy was used in order to generate an APAF-1 -/- mouse. This assay is used to disrupt gene function by creating an intragenic gene fusion. When an APAF-1 gene trap is introduced into cells, many morphological changes occur, such as spina bifida, the persistence of interdigital webs, and open brain. In addition, after embryonic day 12.5, the brain of the embryos showed several structural changes. APAF-1 cells are protected from apoptosis stimuli such as irradiation. A BAX-1 knock-out mouse exhibits normal forebrain formation and
|
{
"page_id": 2457,
"source": null,
"title": "Apoptosis"
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a decreased programmed cell death in some neuronal populations and in the spinal cord, leading to an increase in motor neurons. The caspase proteins are integral parts of the apoptosis pathway, so it follows that knock-outs made have varying damaging results. A caspase 9 knock-out leads to a severe brain malformation . A caspase 8 knock-out leads to cardiac failure and thus embryonic lethality . However, with the use of cre-lox technology, a caspase 8 knock-out has been created that exhibits an increase in peripheral T cells, an impaired T cell response, and a defect in neural tube closure . These mice were found to be resistant to apoptosis mediated by CD95, TNFR, etc. but not resistant to apoptosis caused by UV irradiation, chemotherapeutic drugs, and other stimuli. Finally, a caspase 3 knock-out was characterized by ectopic cell masses in the brain and abnormal apoptotic features such as membrane blebbing or nuclear fragmentation . A remarkable feature of these KO mice is that they have a very restricted phenotype: Casp3, 9, APAF-1 KO mice have deformations of neural tissue and FADD and Casp 8 KO showed defective heart development, however, in both types of KO other organs developed normally and some cell types were still sensitive to apoptotic stimuli suggesting that unknown proapoptotic pathways exist. == Methods for distinguishing apoptotic from necrotic cells == Label-free live cell imaging, time-lapse microscopy, flow fluorocytometry, and transmission electron microscopy can be used to compare apoptotic and necrotic cells. There are also various biochemical techniques for analysis of cell surface markers (phosphatidylserine exposure versus cell permeability by flow cytometry), cellular markers such as DNA fragmentation (flow cytometry), caspase activation, Bid cleavage, and cytochrome c release (Western blotting). Supernatant screening for caspases, HMGB1, and cytokeratin 18 release can identify primary from secondary necrotic cells. However,
|
{
"page_id": 2457,
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no distinct surface or biochemical markers of necrotic cell death have been identified yet, and only negative markers are available. These include absence of apoptotic markers (caspase activation, cytochrome c release, and oligonucleosomal DNA fragmentation) and differential kinetics of cell death markers (phosphatidylserine exposure and cell membrane permeabilization). A selection of techniques that can be used to distinguish apoptosis from necroptotic cells could be found in these references. == Implication in disease == === Defective pathways === The many different types of apoptotic pathways contain a multitude of different biochemical components, many of them not yet understood. As a pathway is more or less sequential in nature, removing or modifying one component leads to an effect in another. In a living organism, this can have disastrous effects, often in the form of disease or disorder. A discussion of every disease caused by modification of the various apoptotic pathways would be impractical, but the concept overlying each one is the same: The normal functioning of the pathway has been disrupted in such a way as to impair the ability of the cell to undergo normal apoptosis. This results in a cell that lives past its "use-by date" and is able to replicate and pass on any faulty machinery to its progeny, increasing the likelihood of the cell's becoming cancerous or diseased. A recently described example of this concept in action can be seen in the development of a lung cancer called NCI-H460. The X-linked inhibitor of apoptosis protein (XIAP) is overexpressed in cells of the H460 cell line. XIAPs bind to the processed form of caspase-9 and suppress the activity of apoptotic activator cytochrome c, therefore overexpression leads to a decrease in the number of proapoptotic agonists. As a consequence, the balance of anti-apoptotic and proapoptotic effectors is upset in favour
|
{
"page_id": 2457,
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of the former, and the damaged cells continue to replicate despite being directed to die. Defects in regulation of apoptosis in cancer cells occur often at the level of control of transcription factors. As a particular example, defects in molecules that control transcription factor NF-κB in cancer change the mode of transcriptional regulation and the response to apoptotic signals, to curtail dependence on the tissue that the cell belongs. This degree of independence from external survival signals, can enable cancer metastasis. ==== Dysregulation of p53 ==== The tumor-suppressor protein p53 accumulates when DNA is damaged due to a chain of biochemical factors. Part of this pathway includes alpha-interferon and beta-interferon, which induce transcription of the p53 gene, resulting in the increase of p53 protein level and enhancement of cancer cell-apoptosis. p53 prevents the cell from replicating by stopping the cell cycle at G1, or interphase, to give the cell time to repair; however, it will induce apoptosis if damage is extensive and repair efforts fail. Any disruption to the regulation of the p53 or interferon genes will result in impaired apoptosis and the possible formation of tumors. === Inhibition === Inhibition of apoptosis can result in a number of cancers, inflammatory diseases, and viral infections. It was originally believed that the associated accumulation of cells was due to an increase in cellular proliferation, but it is now known that it is also due to a decrease in cell death. The most common of these diseases is cancer, the disease of excessive cellular proliferation, which is often characterized by an overexpression of IAP family members. As a result, the malignant cells experience an abnormal response to apoptosis induction: Cycle-regulating genes (such as p53, ras or c-myc) are mutated or inactivated in diseased cells, and further genes (such as bcl-2) also modify
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{
"page_id": 2457,
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their expression in tumors. Some apoptotic factors are vital during mitochondrial respiration e.g. cytochrome C. Pathological inactivation of apoptosis in cancer cells is correlated with frequent respiratory metabolic shifts toward glycolysis (an observation known as the "Warburg hypothesis". ==== HeLa cell ==== Apoptosis in HeLa cells is inhibited by proteins produced by the cell; these inhibitory proteins target retinoblastoma tumor-suppressing proteins. These tumor-suppressing proteins regulate the cell cycle, but are rendered inactive when bound to an inhibitory protein. HPV E6 and E7 are inhibitory proteins expressed by the human papillomavirus, HPV being responsible for the formation of the cervical tumor from which HeLa cells are derived. HPV E6 causes p53, which regulates the cell cycle, to become inactive. HPV E7 binds to retinoblastoma tumor suppressing proteins and limits its ability to control cell division. These two inhibitory proteins are partially responsible for HeLa cells' immortality by inhibiting apoptosis to occur. ==== Treatments ==== The main method of treatment for potential death from signaling-related diseases involves either increasing or decreasing the susceptibility of apoptosis in diseased cells, depending on whether the disease is caused by either the inhibition of or excess apoptosis. For instance, treatments aim to restore apoptosis to treat diseases with deficient cell death and to increase the apoptotic threshold to treat diseases involved with excessive cell death. To stimulate apoptosis, one can increase the number of death receptor ligands (such as TNF or TRAIL), antagonize the anti-apoptotic Bcl-2 pathway, or introduce Smac mimetics to inhibit the inhibitor (IAPs). The addition of agents such as Herceptin, Iressa, or Gleevec works to stop cells from cycling and causes apoptosis activation by blocking growth and survival signaling further upstream. Finally, adding p53-MDM2 complexes displaces p53 and activates the p53 pathway, leading to cell cycle arrest and apoptosis. Many different methods can
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{
"page_id": 2457,
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}
|
be used either to stimulate or to inhibit apoptosis in various places along the death signaling pathway. Apoptosis is a multi-step, multi-pathway cell-death programme that is inherent in every cell of the body. In cancer, the apoptosis cell-division ratio is altered. Cancer treatment by chemotherapy and irradiation kills target cells primarily by inducing apoptosis. === Hyperactive apoptosis === On the other hand, loss of control of cell death (resulting in excess apoptosis) can lead to neurodegenerative diseases, hematologic diseases, and tissue damage. Neurons that rely on mitochondrial respiration undergo apoptosis in neurodegenerative diseases such as Alzheimer's and Parkinson's. (an observation known as the "Inverse Warburg hypothesis"). Moreover, there is an inverse epidemiological comorbidity between neurodegenerative diseases and cancer. The progression of HIV is directly linked to excess, unregulated apoptosis. In a healthy individual, the number of CD4+ lymphocytes is in balance with the cells generated by the bone marrow; however, in HIV-positive patients, this balance is lost due to an inability of the bone marrow to regenerate CD4+ cells. In the case of HIV, CD4+ lymphocytes die at an accelerated rate through uncontrolled apoptosis, when stimulated. At the molecular level, hyperactive apoptosis can be caused by defects in signaling pathways that regulate the Bcl-2 family proteins. Increased expression of apoptotic proteins such as BIM, or their decreased proteolysis, leads to cell death and can cause a number of pathologies, depending on the cells where excessive activity of BIM occurs. Cancer cells can escape apoptosis through mechanisms that suppress BIM expression or by increased proteolysis of BIM. ==== Treatments ==== Treatments aiming to inhibit works to block specific caspases. Finally, the Akt protein kinase promotes cell survival through two pathways. Akt phosphorylates and inhibits Bad (a Bcl-2 family member), causing Bad to interact with the 14-3-3 scaffold, resulting in Bcl dissociation
|
{
"page_id": 2457,
"source": null,
"title": "Apoptosis"
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and thus cell survival. Akt also activates IKKα, which leads to NF-κB activation and cell survival. Active NF-κB induces the expression of anti-apoptotic genes such as Bcl-2, resulting in inhibition of apoptosis. NF-κB has been found to play both an antiapoptotic role and a proapoptotic role depending on the stimuli utilized and the cell type. === HIV progression === The progression of the human immunodeficiency virus infection into AIDS is due primarily to the depletion of CD4+ T-helper lymphocytes in a manner that is too rapid for the body's bone marrow to replenish the cells, leading to a compromised immune system. One of the mechanisms by which T-helper cells are depleted is apoptosis, which results from a series of biochemical pathways: HIV enzymes deactivate anti-apoptotic Bcl-2. This does not directly cause cell death but primes the cell for apoptosis should the appropriate signal be received. In parallel, these enzymes activate proapoptotic procaspase-8, which does directly activate the mitochondrial events of apoptosis. HIV may increase the level of cellular proteins that prompt Fas-mediated apoptosis. HIV proteins decrease the amount of CD4 glycoprotein marker present on the cell membrane. Released viral particles and proteins present in extracellular fluid are able to induce apoptosis in nearby "bystander" T helper cells. HIV decreases the production of molecules involved in marking the cell for apoptosis, giving the virus time to replicate and continue releasing apoptotic agents and virions into the surrounding tissue. The infected CD4+ cell may also receive the death signal from a cytotoxic T cell. Cells may also die as direct consequences of viral infections. HIV-1 expression induces tubular cell G2/M arrest and apoptosis. The progression from HIV to AIDS is not immediate or even necessarily rapid; HIV's cytotoxic activity toward CD4+ lymphocytes is classified as AIDS once a given patient's CD4+ cell
|
{
"page_id": 2457,
"source": null,
"title": "Apoptosis"
}
|
count falls below 200. Researchers from Kumamoto University in Japan have developed a new method to eradicate HIV in viral reservoir cells, named "Lock-in and apoptosis." Using the synthesized compound Heptanoylphosphatidyl L-Inositol Pentakisphophate (or L-Hippo) to bind strongly to the HIV protein PR55Gag, they were able to suppress viral budding. By suppressing viral budding, the researchers were able to trap the HIV virus in the cell and allow for the cell to undergo apoptosis (natural cell death). Associate Professor Mikako Fujita has stated that the approach is not yet available to HIV patients because the research team has to conduct further research on combining the drug therapy that currently exists with this "Lock-in and apoptosis" approach to lead to complete recovery from HIV. === Viral infection === Viral induction of apoptosis occurs when one or several cells of a living organism are infected with a virus, leading to cell death. Cell death in organisms is necessary for the normal development of cells and the cell cycle maturation. It is also important in maintaining the regular functions and activities of cells. Viruses can trigger apoptosis of infected cells via a range of mechanisms including: Receptor binding Activation of protein kinase R (PKR) Interaction with p53 Expression of viral proteins coupled to MHC proteins on the surface of the infected cell, allowing recognition by cells of the immune system (such as natural killer and cytotoxic T cells) that then induce the infected cell to undergo apoptosis. Canine distemper virus (CDV) is known to cause apoptosis in central nervous system and lymphoid tissue of infected dogs in vivo and in vitro. Apoptosis caused by CDV is typically induced via the extrinsic pathway, which activates caspases that disrupt cellular function and eventually leads to the cells death. In normal cells, CDV activates caspase-8 first,
|
{
"page_id": 2457,
"source": null,
"title": "Apoptosis"
}
|
which works as the initiator protein followed by the executioner protein caspase-3. However, apoptosis induced by CDV in HeLa cells does not involve the initiator protein caspase-8. HeLa cell apoptosis caused by CDV follows a different mechanism than that in vero cell lines. This change in the caspase cascade suggests CDV induces apoptosis via the intrinsic pathway, excluding the need for the initiator caspase-8. The executioner protein is instead activated by the internal stimuli caused by viral infection not a caspase cascade. The Oropouche virus (OROV) is found in the family Bunyaviridae. The study of apoptosis brought on by Bunyaviridae was initiated in 1996, when it was observed that apoptosis was induced by the La Crosse virus into the kidney cells of baby hamsters and into the brains of baby mice. OROV is a disease that is transmitted between humans by the biting midge (Culicoides paraensis). It is referred to as a zoonotic arbovirus and causes febrile illness, characterized by the onset of a sudden fever known as Oropouche fever. The Oropouche virus also causes disruption in cultured cells – cells that are cultivated in distinct and specific conditions. An example of this can be seen in HeLa cells, whereby the cells begin to degenerate shortly after they are infected. With the use of gel electrophoresis, it can be observed that OROV causes DNA fragmentation in HeLa cells. It can be interpreted by counting, measuring, and analyzing the cells of the Sub/G1 cell population. When HeLA cells are infected with OROV, the cytochrome C is released from the membrane of the mitochondria, into the cytosol of the cells. This type of interaction shows that apoptosis is activated via an intrinsic pathway. In order for apoptosis to occur within OROV, viral uncoating, viral internalization, along with the replication of cells is
|
{
"page_id": 2457,
"source": null,
"title": "Apoptosis"
}
|
necessary. Apoptosis in some viruses is activated by extracellular stimuli. However, studies have demonstrated that the OROV infection causes apoptosis to be activated through intracellular stimuli and involves the mitochondria. Many viruses encode proteins that can inhibit apoptosis. Several viruses encode viral homologs of Bcl-2. These homologs can inhibit proapoptotic proteins such as BAX and BAK, which are essential for the activation of apoptosis. Examples of viral Bcl-2 proteins include the Epstein-Barr virus BHRF1 protein and the adenovirus E1B 19K protein. Some viruses express caspase inhibitors that inhibit caspase activity and an example is the CrmA protein of cowpox viruses. Whilst a number of viruses can block the effects of TNF and Fas. For example, the M-T2 protein of myxoma viruses can bind TNF preventing it from binding the TNF receptor and inducing a response. Furthermore, many viruses express p53 inhibitors that can bind p53 and inhibit its transcriptional transactivation activity. As a consequence, p53 cannot induce apoptosis, since it cannot induce the expression of proapoptotic proteins. The adenovirus E1B-55K protein and the hepatitis B virus HBx protein are examples of viral proteins that can perform such a function. Viruses can remain intact from apoptosis in particular in the latter stages of infection. They can be exported in the apoptotic bodies that pinch off from the surface of the dying cell, and the fact that they are engulfed by phagocytes prevents the initiation of a host response. This favours the spread of the virus. Prions can cause apoptosis in neurons. == Plants == Programmed cell death in plants has a number of molecular similarities to that of animal apoptosis, but it also has differences, notable ones being the presence of a cell wall and the lack of an immune system that removes the pieces of the dead cell. Instead of
|
{
"page_id": 2457,
"source": null,
"title": "Apoptosis"
}
|
an immune response, the dying cell synthesizes substances to break itself down and places them in a vacuole that ruptures as the cell dies. Additionally, plants do not contain phagocytic cells, which are essential in the process of breaking down and removing apoptotic bodies. Whether this whole process resembles animal apoptosis closely enough to warrant using the name apoptosis (as opposed to the more general programmed cell death) is unclear. == Caspase-independent apoptosis == The characterization of the caspases allowed the development of caspase inhibitors, which can be used to determine whether a cellular process involves active caspases. Using these inhibitors it was discovered that cells can die while displaying a morphology similar to apoptosis without caspase activation. Later studies linked this phenomenon to the release of AIF (apoptosis-inducing factor) from the mitochondria and its translocation into the nucleus mediated by its NLS (nuclear localization signal). Inside the mitochondria, AIF is anchored to the inner membrane. In order to be released, the protein is cleaved by a calcium-dependent calpain protease. == See also == == Explanatory footnotes == == Citations == == General bibliography == == External links == Apoptosis & Caspase 3, The Proteolysis Map – animation Apoptosis & Caspase 8, The Proteolysis Map – animation Apoptosis & Caspase 7, The Proteolysis Map – animation Apoptosis MiniCOPE Dictionary – list of apoptosis terms and acronyms Apoptosis (Programmed Cell Death) – The Virtual Library of Biochemistry, Molecular Biology and Cell Biology Archived 2021-04-25 at the Wayback Machine Apoptosis Research Portal Apoptosis Info Apoptosis protocols, articles, news, and recent publications. Database of proteins involved in apoptosis Apoptosis Video Apoptosis Video (WEHI on YouTube ) The Mechanisms of Apoptosis Archived 2018-03-09 at the Wayback Machine Kimball's Biology Pages. Simple explanation of the mechanisms of apoptosis triggered by internal signals (bcl-2), along the
|
{
"page_id": 2457,
"source": null,
"title": "Apoptosis"
}
|
caspase-9, caspase-3 and caspase-7 pathway; and by external signals (FAS and TNF), along the caspase 8 pathway. Accessed 25 March 2007. WikiPathways – Apoptosis pathway Archived 2008-09-16 at the Wayback Machine "Finding Cancer's Self-Destruct Button". CR magazine (Spring 2007). Article on apoptosis and cancer. Xiaodong Wang's lecture: Introduction to Apoptosis Archived 2013-10-29 at the Wayback Machine Robert Horvitz's Short Clip: Discovering Programmed Cell Death The Bcl-2 Database Archived 2013-10-23 at the Wayback Machine DeathBase: a database of proteins involved in cell death, curated by experts European Cell Death Organization Apoptosis signaling pathway created by Cusabio
|
{
"page_id": 2457,
"source": null,
"title": "Apoptosis"
}
|
Photothermal time (PTT) is a product between growing degree-days (GDD) and day length (hours) for each day. PTT = GDD × DL It can be used to quantify environment, as well as the timing of developmental stages of plants. == References ==
|
{
"page_id": 57674142,
"source": null,
"title": "Photothermal time"
}
|
The Olin Raschig process is a chemical process for the production of hydrazine. The main steps in this process, patented by German chemist Friedrich Raschig in 1906 and one of three reactions named after him, are the formation of monochloramine from ammonia and hypochlorite, and the subsequent reaction of monochloramine with ammonia towards hydrazine. The process was further optimised and used by the Olin Corporation for the production of anhydrous hydrazine for aerospace applications. == Process == The commercially used Olin Raschig process consists of the following steps: First, sodium hypochlorite solution is mixed with a threefold excess of ammonia at 5 °C to give monochloramine. The primary reaction proceeds according to the idealised equation NaOCl + NH3 → NH2Cl + NaOH The monochloramine solution is then added to a 30-fold excess of ammonia at 130 °C and elevated pressure, causing a second reaction NH2Cl + NH3 → N2H4 + HCl The hydrochloric acid and sodium hydroxide byproducts undergo a secondary reaction to release the byproducts of water and sodium chloride. The overall reaction is thus NaOCl + 2NH3 → N2H4 + NaCl + H2O Excess ammonia and sodium chloride are removed by distillation, followed by azeotropic distillation with aniline to remove water. == References ==
|
{
"page_id": 1116577,
"source": null,
"title": "Olin Raschig process"
}
|
Andrey Lvovich Kursanov (Russian: Андрей Львович Курсанов; 8 November 1902 – 20 September 1999) was a Soviet specialist on the physiology and biochemistry of plants. He was an academician of the Soviet and Russian Academies of Sciences since 1953. He was a member of the Presidium of the Academy of Sciences of the Soviet Union in 1957–1963. Kursanov graduated from Moscow State University in 1926. He was awarded the degree of Doctor of Sciences in biology in 1940 and became a professor at his alma mater in 1944. In 1954, Kursanov and Boris Rybakov represented the Soviet Academy of Sciences at the Columbia University Bicentennial in New York City. Professor Kursanov was awarded a number of honorary doctorates and was an honorary member of a number of foreign scientific societies and academies. He was elected a foreign fellow of the American Academy of Arts and Sciences in 1962 and member of the Polish Academy of Sciences in 1965. == Awards and honors == Hero of Socialist Labour (1969) Order of Lenin, four times (1953, 1969, 1972, 1975) Order of the October Revolution (1982) Order of the Red Banner of Labour, twice (1945, 1962) Lomonosov Gold Medal (1983) == References ==
|
{
"page_id": 9898403,
"source": null,
"title": "Andrey Kursanov"
}
|
French Zoosemiotics Society (French: Société Française de Zoosémiotique) is an academic society, uniting ethologists, zoologists, semioticians (including biosemioticians and ecosemioticians), linguists, veterinarians and philosophers, and promoting a semiotic approach in zoosemiotics and animal studies. The focus of the society is to promote and facilitate research in animal communication, their intraspecific and interspecific sign systems, as well as human-animal communication studies. The Society was established in 2018 by scholars of Sorbonne University, National Museum of Natural History, and other universities and institutions of France. This is seemingly the first zoosemiotics society in the world. The founding president of the Society is Astrid Guillaume. == See also == International Society for Biosemiotic Studies == References == == External links == The Society’s website Jane Goodall Institute France. SfZ youtube channel.
|
{
"page_id": 77859236,
"source": null,
"title": "French Zoosemiotics Society"
}
|
The posterior intermuscular septum of leg or posterior crural intermuscular septum is a band of fascia which separates the lateral compartment of leg. The deep fascia of leg gives off from its deep surface, on the lateral side of the leg, two strong intermuscular septa, the anterior and posterior peroneal septa, which enclose the peronæi longus and brevis, and separate them from the muscles of the anterior and posterior crural regions, and several more slender processes which enclose the individual muscles in each region. == References == This article incorporates text in the public domain from page 480 of the 20th edition of Gray's Anatomy (1918) == External links == Horizontal section through the middle of the leg from www.dartmouth.edu
|
{
"page_id": 15337892,
"source": null,
"title": "Posterior intermuscular septum of leg"
}
|
Chemistry: A Volatile History is a 2010 BBC documentary on the history of chemistry presented by Jim Al-Khalili. It was nominated for the 2010 British Academy Television Awards in the category Specialist Factual. == Episode 1: Discovering the Elements == === Introduction === Only in the last 200 years have we known what an element is – a substance that cannot be broken down further by chemical reaction. The Ancient Greeks, with no way of breaking open substances, could only base their ideas of the elements on what they could see: Earth, Fire, Water and Air. In the 16th century alchemists were busy trying to turn base metals like lead, into gold. === Paracelsus and the tria prima === It was the Swiss alchemist and surgeon Paracelsus who first challenged the Ancient Greek idea of four elements. In 1526 Paracelsus was in Basel, when the famous printer Frobenius was told he would have to have his leg amputated in a life-saving operation. Instead of accepting the received wisdom, he called upon Paracelsus who cured him in the unconventional way of using his alchemical knowledge. This established him as a radical thinker, giving weight to his ideas, principal amongst which was the idea that the world was actually made of three elements: the tria prima comprising salt, sulphur and mercury. Paracelsus did not succeed in convincing the establishment – instead he managed to enrage them by burning their established medical texts, and eventually had to flee Switzerland for Germany. It was, however, the alchemical pursuit for gold that led to the first breakthrough in the hunt for new elements. === Hennig Brand and the icy noctiluca === In 1669 Hennig Brand was looking for a way of extracting gold from the human body, and struck upon the idea of using urine,
|
{
"page_id": 29952420,
"source": null,
"title": "Chemistry: A Volatile History"
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|
thinking that urine might contain some part of the 'life force' vital to sustaining human life. To get rid of the unimportant parts, primarily water, Brand boiled the urine for several days until he was left with a thick paste. Finally, fragments of a substance emerged which burned brighter than any Medieval candle available at the time, but which left the vessel it burnt in cold: Brand named this new substance icy noctiluca – 'cold night light'. Soon after its discovery, icy noctiluca toured the Royal Houses of Europe and in 1677 it came before the Royal Society in London, then under the chairmanship of Charles II, where one of its members decided to investigate. In his book New Experiments and Observations Made Upon the Icy Noctiluca Robert Boyle describes an experiment in which sulphur and phosphorus powders are mixed causing them to burn fiercely. This discovery was the basis for the invention of the match. Phosphorus, as icy noctiluca is now known, is used in everything from match heads to toothpaste and ultimately in the Second World War bombs which destroyed the very city in which Brand discovered it – Hamburg. Whilst Brand never discovered gold, his accidental discovery of the element now known as phosphorus gave rise to the idea that elements could be hidden inside other substances. === Robert Boyle and The Sceptical Chymist === More than a decade earlier in 1661, a year after the Royal Society opened, Boyle deposited The Sceptical Chymist in its vaults. This book is usually regarded as the turning point that signaled the transition from alchemy to chemistry. The Sceptical Chymist was innovative in several ways: it was not written in Latin, as had been the tradition for alchemist books, but in English; it dispensed with the old chemical symbols for
|
{
"page_id": 29952420,
"source": null,
"title": "Chemistry: A Volatile History"
}
|
various elements, using English names instead; and most crucially it was actually published, as opposed to kept secret. Boyle was willing to share his discoveries to allow others to build on his work and further the scientific understanding of the elements. He wanted to put alchemy on a more scientific footing – ditching the metaphysical baggage it had brought with it from the previous century. Unfortunately, this new age of chemical enlightenment was fraught with blind alleys. === Johann Becher and phlogiston === In 1667 the German scientist Johann Becker proposed that fire was caused by an ethereal, odourless, tasteless, colourless, weightless entity called phlogiston. The idea was that phlogiston causes things to burn, reducing them to their pure form. For example, burning wood releases phlogiston, leaving the pure form of wood – ash, therefore wood is composed of ash (pure wood) and phlogiston. Phlogiston was accepted as scientific truth, paralysing the scientific community's ability to discover more, true elements. One scientist even claimed to have isolated phlogiston. === Henry Cavendish and inflammable air === A major shareholder in the Bank of England with royal connections, Henry Cavendish was a painfully shy character, who made the vital chemical contribution of discovering the first elemental gas. He added some zinc to spirit of salt (hydrochloric acid) and collected the evanescence given off as bubbles. The gas he collected was tasteless, odourless and colourless, and moreover it produced a squeaky pop in the presence of a flame – this led Cavendish to name the gas inflammable air, which he believed to be one and the same as phlogiston. Cavendish, though he did not realise it, made an important observation about burning phlogiston in air; a dewy liquid was formed on the inside of the glassware: water. This should have had enormous repercussions
|
{
"page_id": 29952420,
"source": null,
"title": "Chemistry: A Volatile History"
}
|
for the whole scientific community in the 1700s, who still believed water to be an elemental substance. Yet, if water could be made by burning inflammable air, then water is not an element, but a compound. However, it simply did not occur to Cavendish that water was a compound – instead he assumed that the airs contained a form of water, which phlogiston modified into liquid, elemental water. Phlogiston had given the Ancient Greek idea of water as an element a brief reprieve, but the Greek system was now under heavy scrutiny as the Royal Society commissioned its members to investigate the invisible airs. === Joseph Priestley and dephlogisticated air === By the mid-1700s there were three known 'airs': Common air – the air we breathe; Cavendish's inflammable air; Fixed air. It was this last air which caught the attention of Joseph Priestley, a Unitarian minister whose favourite pastime was the investigation of airs – specifically, fixed air, given off by the fermentation process in breweries. Priestley's passion for science led to an invitation to Bowood House, to tutor the children of Lord Shelburne. This was an excellent opportunity, given that Priestley did not have the money of earlier chemists like Boyle and Cavendish, and would still be free to pursue his own research. In 1774 Priestley performed a hugely important experiment: he heated mercuric calc and collected the gas given off. He discovered that this gas was able to relight the embers of a previously lit wooden splint. He concluded that the splint was introducing phlogiston to the gas, only after which could it burn, therefore the gas must be 'without phlogiston' – this led Priestley to name it dephlogisticated air. In October 1775 Priestley accompanied Lord Shelburne on a trip to Paris where they were invited to dine
|
{
"page_id": 29952420,
"source": null,
"title": "Chemistry: A Volatile History"
}
|
with the preeminent scientists of the time. It is here that Priestley met the French scientist Antoine Lavoisier. === Antoine Lavoisier and the end of phlogiston === Priestley told Lavoisier all the details of his experiments upon the production of dephlogisticated air. Unlike Priestley, Lavoisier had one of the best equipped laboratories in Europe and now turned his attention to the highly accurate measurement of the masses of substances before and after they were heated. Lavoisier weighted a sample of tin, then reweighed after he had heated it and found it had increased in mass. This was an unexpected result given that the tin was thought to have released phlogiston during the burning process. Lavoisier was struck with a ground-breaking thought – maybe the tin had absorbed something from the air, making it heavier, but if so, what? To investigate this further, Lavoisier reran Priestley's experiment in reverse – he heated some mercury in a sealed container until it turned into mercuric calc and measured the amount of air absorbed. He then heated the mercuric calc and measured the amount of air released and discovered the quantities were the same. Lavoisier realised that something was absorbed from the air when mercury was heated to make mercuric calc, and that same gas was released when the mercuric calc was heated. Lavoisier concluded that this gas was unrelated to phlogiston, but was in fact a brand new element, which he named oxygen. Lavoisier had successfully dispensed with the need for the theory of phlogiston and recognised Priestley's 'dephlogisticated air' as the element oxygen. Despite the fact it was Priestley's original work that laid the foundations for his discovery, Lavoisier claimed he had discovered oxygen; Priestley, after all, had failed to recognise it as a new element. Lavoisier went on to give science
|
{
"page_id": 29952420,
"source": null,
"title": "Chemistry: A Volatile History"
}
|
its first definition of an element: a substance that cannot be decomposed by existing chemical means. He also set about drawing up a list of all the elements – now 33 elements replaced the ancient four. His list was grouped into four categories: gases, non-metals, metals and earths. On top of this, Lavoisier created a classification system for the ever-increasing array of chemicals being discovered. As mentioned, 'dephlogisticated air' became oxygen, 'inflammable air' became hydrogen, but the nomenclature of compounds was also put on a more logical footing as 'oil of vitriol' became sulphuric acid, 'philosophical wool' became zinc oxide and 'astringent mars saffron' became iron oxide. Unfortunately, whilst Lavoisier had rid the world of the phlogiston paradigm, he introduced two new erroneous elements now known to be pure energy: lumière and calorique; light and heat. In revenge for his sympathies with the revolutionaries in France, Priestley's home in England was targeted by arsonists in 1791, luckily he escaped thanks to a tip-off, but decided to flee to America. Lavoisier's contributions to science were cut short in 1794 by the revolutionaries, who arrested him on grounds of being an enemy of the French people, and had him guillotined. === Humphry Davy and potash === In 1807, the Professor of Chemistry at the Royal Institution in London was the Cornishman Humphry Davy. He was investigating crystalline salts of potash because he was unconvinced potash was an element, but by the end of the previous century, Lavoisier had been unable to break it down further. Since then however, the first electric battery had recently been invented (rows of metal plates and cardboard soaked in saltwater). Although scientists were aware that the production of a continuous electric current was due to some property of the metals, Davy believed that a chemical reaction was
|
{
"page_id": 29952420,
"source": null,
"title": "Chemistry: A Volatile History"
}
|
taking place. If that was true, then maybe the reverse was also true: an electric current could cause a chemical reaction. Davy heated the potash until it was liquid, then introduced two electrodes and passed a current through the molten potash. A lilac flame was observed, the result of successfully breaking down potash into its constituent elements – one of which, was the previously never before seen element potassium. Davy went on to add six new elements to Lavoisier's list, as well as confirming that substances like chlorine and iodine were also elements. By the time of his death in 1829 the idea of the elements was firmly established, 55 separate elements had been discovered, and the world had a new science: Chemistry. == Episode 2: The Order of the Elements == === Introduction === At the beginning of the 19th century only 55 of the 92 naturally occurring elements had been discovered. Scientists had no idea how many more they might find, or indeed if there were an infinite number of elements. They also sought to answer a fundamental question, namely: is there a pattern to the elements? === John Dalton's atoms === Scientists had recently discovered that when elements combine to form compounds, they always do so in the same proportions, by weight. John Dalton thought that for this to happen, each element had to be made of its own unique building blocks, which he called atoms. Dalton suggested that everything in the universe was made of atoms, and that there are as many kinds of atoms as there are elements, each one with its own signature weight. Based on these ideas, working completely alone, Dalton attempted to impose some order on the elements by drawing up a list, where each element was represented by an alchemical-looking symbol,
|
{
"page_id": 29952420,
"source": null,
"title": "Chemistry: A Volatile History"
}
|
ordered by atomic weight. Although Dalton did not get all his atomic weights correct, he was pointing science in the right direction. Sadly, in the early 1800s few scientists accepted the idea that elements had different weights. === Jöns Jacob Berzelius' pursuit of atomic weights === The Swedish scientist Jöns Jacob Berzelius was one of the few scientists who strongly believed in the idea of atomic weights, and thought that knowing as much as possible about their weights was vitally important. When he heard of Dalton's theory, he set about the gargantuan task of measuring the atomic weight of every single known element – without any proof that Dalton's atoms actually existed. This was even more challenging than it first seems once you consider the fact that very little of the chemical glassware necessary for such precise measurements had been invented. Berzelius had to manufacture much of it himself. Berzelius' experiences with glass-blowing had an additional bonus, in 1824 he discovered that one of the constituents of glass was a new element – silicon. Having already discovered three other elements prior to silicon: thorium, cerium and selenium, Berzelius spent the next ten years obsessively measuring more than two thousand chemical compounds in pursuit of accurate atomic weights for the elements. Eventually Berzelius had remarkably accurate atomic weights for 45 elements; his value for chlorine was accurate to within 0.2% of the value we know today. However, by the time Berzelius had produced his results, other scientists were now measuring atomic weights – and getting conflicting results. In fact, scientists were looking for all sorts of patterns throughout the elements. === Johann Döbereiner's triads === One such pattern hunter was German chemist Johann Döbereiner. He believed the key to understanding the elements lay not with their atomic weights but with their
|
{
"page_id": 29952420,
"source": null,
"title": "Chemistry: A Volatile History"
}
|
chemical properties. He noticed that one could often single out three elements that exhibited similar properties, such as the alkali metals, which he called triads. The problem was that Döbereiner's triads only worked for a few of the elements and got scientists no further than atomic weights. === Dmitri Mendeleev moves to St Petersburg === In 1848 a huge fire destroyed the factory of the widow Maria Mendeleeva. Facing destitution she decided to embark on the 1,300 mile journey from Western Siberia to St Petersburg – walking a significant portion of the route – so her son Dmitri Mendeleev could continue his education in the capital of the Russian Empire. At the time the scientific community was grappling with the problem of how to bring order to the 63 elements that were now known. Mendeleev was still a student when he attended the world's first international chemistry congress – convened to settle the confusion surrounding atomic weights. === Stanislao Cannizzaro's standard for measuring atomic weights === Sicilian chemist Stanislao Cannizzaro was still convinced that atomic weights held the key to the order of the elements and had found a new way of measuring them. Cannizzaro knew that equal volumes of gases contain equal numbers of particles, therefore instead of working with solids and liquids and all the unreliability that entails, he proposed measuring the densities of gases to measure the weights of individual gaseous atoms. Whereas Berzelius' results had failed to convince anyone, Cannizzaro's method set an agreed standard for measuring atomic weights accurately. Chemists soon found that even with accurate atomic weights, the elements still seemed unordered, but then, a solitary English chemist made a curious discovery. === John Newlands' octaves === In 1863 John Newlands noticed that when ordered by weight, every eighth element seemed to share similar
|
{
"page_id": 29952420,
"source": null,
"title": "Chemistry: A Volatile History"
}
|
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