1.
Moiety (chemistry)
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In organic chemistry moiety is a term used for part of a molecule. Larger moieties are often functional groups, a functional group is a moiety that participates in similar chemical reactions in most molecules that contain it. In turn the parts of the group are termed moieties, for example, methyl p-hydroxybenzoate contains a phenol functional group within the acyl moiety, which in turn is part of the paraben moiety. Moieties that are branches extending from the backbone of a hydrocarbon molecule, which can often be broken off and substituted with others, are called substituents or side chains
2.
Hydroxy group
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A hydroxy or hydroxyl group is the entity with the formula OH. It contains oxygen bonded to hydrogen, in organic chemistry, alcohol and carboxylic acids contain hydroxy groups. The anion, called hydroxide, consists of a hydroxy group, according to IUPAC rules, the term hydroxyl refers to the radical OH only, while the functional group −OH is called hydroxy group. Water, alcohols, carboxylic acids, and many other hydroxy-containing compounds can be deprotonated readily and this behavior is rationalized by the disparate electronegativities of oxygen and hydrogen. Hydroxy-containing compounds engage in hydrogen bonding, which causes them to stick together, organic compounds, which are often poorly soluble in water, become water soluble when they contain two or more hydroxy groups, as illustrated by sugars and amino acid. The hydroxy group is pervasive in chemistry and biochemistry, many inorganic compounds contain hydroxy groups, including sulfuric acid, the chemical compound produced on the largest scale industrially. Hydroxy groups participate in the reactions that link simple biological molecules into long chains. The joining of a fatty acid to glycerol to form a triacylglycerol removes the −OH from the end of the fatty acid. The joining of two aldehyde sugars to form a disaccharide removes the −OH from the group at the aldehyde end of one sugar. The creation of a bond to link two amino acids to make a protein removes the −OH from the carboxy group of one amino acid. Hydroxyl radicals are highly reactive and undergo chemical reactions that make them short-lived, when biological systems are exposed to hydroxyl radicals, they can cause damage to cells, including those in humans, where they react with DNA, lipids, and proteins. In 2009, Indias Chandrayaan-1 satellite, NASAs Cassini spacecraft and the Deep Impact probe have each detected the presence of water by evidence of hydroxyl fragments on the Moon. As reported by Richard Kerr, A spectrometer detected an infrared absorption at a wavelength of 3.0 micrometers that only water or hydroxyl—a hydrogen, NASA also reported in 2009 that the LCROSS probe revealed an ultraviolet emission spectrum consistent with hydroxyl presence. The Venus Express orbiter sent back Venus science data from April 2006 until December 2014, results from Venus Express include the detection of hydroxyl in the atmosphere. Hydronium Ion Oxide Reece, Jane, Urry, Lisa, Cain, Michael, Wasserman, Steven, Minorsky, Peter, Jackson, berge, Susan, Golden, Brandy, Triglia, Logan
3.
Alkyl
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In organic chemistry, an alkyl substituent is an alkane missing one hydrogen. The term alkyl is intentionally unspecific to include many possible substitutions, an acyclic alkyl has the general formula CnH2n+1. A cycloalkyl is derived from a cycloalkane by removal of an atom from a ring and has the general formula CnH2n-1. Typically an alkyl is a part of a larger molecule, in structural formula, the symbol R is used to designate a generic alkyl group. The smallest alkyl group is methyl, with the formula CH3−, the word root alkyl is encountered in several contexts. Alkylation is an important operation in refineries, for example in the production of high-octane gasoline, alkylating antineoplastic agents refer to a class of compounds that are used to treat cancer. In such case, the alkyl is used loosely. For example, nitrogen mustards are well-known alkylating agents, but they are more complex than a mere hydrocarbon, in chemistry, alkyl refers to a group, a substituent, that is attached to other molecular fragments. For example, alkyl lithium reagents have the empirical formula Li, a dialkyl ether is an ether with two alkyl groups, e. g. diethyl ether. In medicinal chemistry, the incorporation of alkyl chains into some chemical compounds increases their lipophilicity and this strategy has been used to increase the antimicrobial activity of flavanones and chalcones. Usually alkyl groups are attached to atoms or groups of atoms. Free alkyls occur as neutral compounds, as anions, or as cations, the neutral alkyl free radicals have no special name. Such species are encountered only as transient intermediates, but some are quite stable. Typically alkyl cations are generated using super acids, alkyl anions are observed in the presence of strong bases, alkyls are commonly observed in mass spectrometry of organic compounds. The simplest series have the general formula CnH2n+1, alkyls include methyl, CH3·, ethyl, propyl, butyl, pentyl, and so on. Alkyl groups that one ring have the formula CnH2n−1, e. g. cyclopropyl and cyclohexyl. First, five atoms comprise the longest straight chain of carbon centers, the parent five-carbon compound is named pentane. The methyl substituent or group is highlighted red, according to the usual rules of nomenclature, alkyl groups are included in the name of the molecule before the root, as in methylpentane
4.
Organic chemistry
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Study of structure includes many physical and chemical methods to determine the chemical composition and the chemical constitution of organic compounds and materials. In the modern era, the range extends further into the table, with main group elements, including, Group 1 and 2 organometallic compounds. They either form the basis of, or are important constituents of, many products including pharmaceuticals, petrochemicals and products made from them, plastics, fuels and explosives. Before the nineteenth century, chemists generally believed that compounds obtained from living organisms were endowed with a force that distinguished them from inorganic compounds. According to the concept of vitalism, organic matter was endowed with a vital force, during the first half of the nineteenth century, some of the first systematic studies of organic compounds were reported. Around 1816 Michel Chevreul started a study of soaps made from various fats and he separated the different acids that, in combination with the alkali, produced the soap. Since these were all compounds, he demonstrated that it was possible to make a chemical change in various fats, producing new compounds. In 1828 Friedrich Wöhler produced the chemical urea, a constituent of urine, from inorganic starting materials. The event is now accepted as indeed disproving the doctrine of vitalism. In 1856 William Henry Perkin, while trying to manufacture quinine accidentally produced the organic dye now known as Perkins mauve and his discovery, made widely known through its financial success, greatly increased interest in organic chemistry. A crucial breakthrough for organic chemistry was the concept of chemical structure, ehrlich popularized the concepts of magic bullet drugs and of systematically improving drug therapies. His laboratory made decisive contributions to developing antiserum for diphtheria and standardizing therapeutic serums, early examples of organic reactions and applications were often found because of a combination of luck and preparation for unexpected observations. The latter half of the 19th century however witnessed systematic studies of organic compounds, the development of synthetic indigo is illustrative. The production of indigo from plant sources dropped from 19,000 tons in 1897 to 1,000 tons by 1914 thanks to the methods developed by Adolf von Baeyer. In 2002,17,000 tons of indigo were produced from petrochemicals. In the early part of the 20th Century, polymers and enzymes were shown to be large organic molecules, the multiple-step synthesis of complex organic compounds is called total synthesis. Total synthesis of natural compounds increased in complexity to glucose. For example, cholesterol-related compounds have opened ways to synthesize complex human hormones, since the start of the 20th century, complexity of total syntheses has been increased to include molecules of high complexity such as lysergic acid and vitamin B12
5.
IUPAC
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The International Union of Pure and Applied Chemistry /ˈaɪjuːpæk/ or /ˈjuːpæk/ is an international federation of National Adhering Organizations that represents chemists in individual countries. It is a member of the International Council for Science, IUPAC is registered in Zürich, Switzerland, and the administrative office, known as the IUPAC Secretariat, is in Research Triangle Park, North Carolina, United States. This administrative office is headed by IUPACs executive director, currently Lynn Soby, IUPAC was established in 1919 as the successor of the International Congress of Applied Chemistry for the advancement of chemistry. Its members, the National Adhering Organizations, can be national chemistry societies, national academies of sciences, there are fifty-four National Adhering Organizations and three Associate National Adhering Organizations. IUPACs Inter-divisional Committee on Nomenclature and Symbols is the world authority in developing standards for the naming of the chemical elements. Since its creation, IUPAC has been run by different committees with different responsibilities. These committees run different projects which include standardizing nomenclature, finding ways to bring chemistry to the world, IUPAC is best known for its works standardizing nomenclature in chemistry and other fields of science, but IUPAC has publications in many fields including chemistry, biology and physics. IUPAC is also known for standardizing the atomic weights of the elements through one of its oldest standing committees, the need for an international standard for chemistry was first addressed in 1860 by a committee headed by German scientist Friedrich August Kekulé von Stradonitz. This committee was the first international conference to create an international naming system for organic compounds, the ideas that were formulated in that conference evolved into the official IUPAC nomenclature of organic chemistry. IUPAC stands as a legacy of this meeting, making it one of the most important historical international collaborations of chemistry societies, since this time, IUPAC has been the official organization held with the responsibility of updating and maintaining official organic nomenclature. IUPAC as such was established in 1919, one notable country excluded from this early IUPAC is Germany. Germanys exclusion was a result of prejudice towards Germans by the Allied powers after World War I, Germany was finally admitted into IUPAC during 1929. However, Nazi Germany was removed from IUPAC during World War II, during World War II, IUPAC was affiliated with the Allied powers, but had little involvement during the war effort itself. After the war, East and West Germany were eventually readmitted to IUPAC, since World War II, IUPAC has been focused on standardizing nomenclature and methods in science without interruption. In 2016, IUPAC denounced the use of chlorine as a chemical weapon, the letter stated, Our organizations deplore the use of chlorine in this manner. According to the CWC, the use, stockpiling, distribution, IUPAC is governed by several committees that all have different responsibilities. Each committee is made up of members of different National Adhering Organizations from different countries, the steering committee hierarchy for IUPAC is as follows, All committees have an allotted budget to which they must adhere. Any committee may start a project, if a projects spending becomes too much for a committee to continue funding, it must take the issue to the Project Committee
6.
Carboxylic acid
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A carboxylic acid /ˌkɑːrbɒkˈsɪlɪk/ is an organic compound that contains a carboxyl group. The general formula of an acid is R–COOH, with R referring to the rest of the molecule. Carboxylic acids occur widely and include the amino acids and acetic acid, salts and esters of carboxylic acids are called carboxylates. When a carboxyl group is deprotonated, its conjugate base forms a carboxylate anion, carboxylate ions are resonance-stabilized, and this increased stability makes carboxylic acids more acidic than alcohols. Carboxylic acids can be seen as reduced or alkylated forms of the Lewis acid carbon dioxide, carboxylic acids are commonly identified using their trivial names, and usually have the suffix -ic acid. IUPAC-recommended names also exist, in system, carboxylic acids have an -oic acid suffix. For example, butyric acid is butanoic acid by IUPAC guidelines, the -oic acid nomenclature detail is based on the name of the previously-known chemical benzoic acid. Alternately, it can be named as a carboxy or carboxylic acid substituent on another parent structure, for example, 2-carboxyfuran. The carboxylate anion of an acid is usually named with the suffix -ate, in keeping with the general pattern of -ic acid and -ate for a conjugate acid and its conjugate base. For example, the base of acetic acid is acetate. The radical •COOH has only a fleeting existence. The acid dissociation constant of •COOH has been measured using electron paramagnetic resonance spectroscopy, the carboxyl group tends to dimerise to form oxalic acid. Because they are both hydrogen-bond acceptors and hydrogen-bond donors, they participate in hydrogen bonding. Together the hydroxyl and carbonyl group forms the functional group carboxyl, carboxylic acids usually exist as dimeric pairs in nonpolar media due to their tendency to self-associate. Smaller carboxylic acids are soluble in water, whereas higher carboxylic acids are less due to the increasing hydrophobic nature of the alkyl chain. These longer chain acids tend to be soluble in less-polar solvents such as ethers. Carboxylic acids tend to have higher boiling points than water, not only because of their surface area. Carboxylic acids tend to evaporate or boil as these dimers, for boiling to occur, either the dimer bonds must be broken or the entire dimer arrangement must be vaporised, both of which increase the enthalpy of vaporization requirements significantly
7.
Carbon
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Carbon is a chemical element with symbol C and atomic number 6. It is nonmetallic and tetravalent—making four electrons available to form covalent chemical bonds, three isotopes occur naturally, 12C and 13C being stable, while 14C is a radioactive isotope, decaying with a half-life of about 5,730 years. Carbon is one of the few elements known since antiquity, Carbon is the 15th most abundant element in the Earths crust, and the fourth most abundant element in the universe by mass after hydrogen, helium, and oxygen. It is the second most abundant element in the body by mass after oxygen. The atoms of carbon can bond together in different ways, termed allotropes of carbon, the best known are graphite, diamond, and amorphous carbon. The physical properties of carbon vary widely with the allotropic form, for example, graphite is opaque and black while diamond is highly transparent. Graphite is soft enough to form a streak on paper, while diamond is the hardest naturally occurring material known, graphite is a good electrical conductor while diamond has a low electrical conductivity. Under normal conditions, diamond, carbon nanotubes, and graphene have the highest thermal conductivities of all known materials, all carbon allotropes are solids under normal conditions, with graphite being the most thermodynamically stable form. They are chemically resistant and require high temperature to react even with oxygen, the most common oxidation state of carbon in inorganic compounds is +4, while +2 is found in carbon monoxide and transition metal carbonyl complexes. The largest sources of carbon are limestones, dolomites and carbon dioxide, but significant quantities occur in organic deposits of coal, peat, oil. For this reason, carbon has often referred to as the king of the elements. The allotropes of carbon graphite, one of the softest known substances, and diamond. It bonds readily with other small atoms including other carbon atoms, Carbon is known to form almost ten million different compounds, a large majority of all chemical compounds. Carbon also has the highest sublimation point of all elements, although thermodynamically prone to oxidation, carbon resists oxidation more effectively than elements such as iron and copper that are weaker reducing agents at room temperature. Carbon is the element, with a ground-state electron configuration of 1s22s22p2. Its first four ionisation energies,1086.5,2352.6,4620.5 and 6222.7 kJ/mol, are higher than those of the heavier group 14 elements. Carbons covalent radii are normally taken as 77.2 pm,66.7 pm and 60.3 pm, although these may vary depending on coordination number, in general, covalent radius decreases with lower coordination number and higher bond order. Carbon compounds form the basis of all life on Earth
8.
Oxygen
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Oxygen is a chemical element with symbol O and atomic number 8. It is a member of the group on the periodic table and is a highly reactive nonmetal. By mass, oxygen is the third-most abundant element in the universe, after hydrogen, at standard temperature and pressure, two atoms of the element bind to form dioxygen, a colorless and odorless diatomic gas with the formula O2. This is an important part of the atmosphere and diatomic oxygen gas constitutes 20. 8% of the Earths atmosphere, additionally, as oxides the element makes up almost half of the Earths crust. Most of the mass of living organisms is oxygen as a component of water, conversely, oxygen is continuously replenished by photosynthesis, which uses the energy of sunlight to produce oxygen from water and carbon dioxide. Oxygen is too reactive to remain a free element in air without being continuously replenished by the photosynthetic action of living organisms. Another form of oxygen, ozone, strongly absorbs ultraviolet UVB radiation, but ozone is a pollutant near the surface where it is a by-product of smog. At low earth orbit altitudes, sufficient atomic oxygen is present to cause corrosion of spacecraft, the name oxygen was coined in 1777 by Antoine Lavoisier, whose experiments with oxygen helped to discredit the then-popular phlogiston theory of combustion and corrosion. One of the first known experiments on the relationship between combustion and air was conducted by the 2nd century BCE Greek writer on mechanics, Philo of Byzantium. In his work Pneumatica, Philo observed that inverting a vessel over a burning candle, Philo incorrectly surmised that parts of the air in the vessel were converted into the classical element fire and thus were able to escape through pores in the glass. Many centuries later Leonardo da Vinci built on Philos work by observing that a portion of air is consumed during combustion and respiration, Oxygen was discovered by the Polish alchemist Sendivogius, who considered it the philosophers stone. In the late 17th century, Robert Boyle proved that air is necessary for combustion, English chemist John Mayow refined this work by showing that fire requires only a part of air that he called spiritus nitroaereus. From this he surmised that nitroaereus is consumed in both respiration and combustion, Mayow observed that antimony increased in weight when heated, and inferred that the nitroaereus must have combined with it. Accounts of these and other experiments and ideas were published in 1668 in his work Tractatus duo in the tract De respiratione. Robert Hooke, Ole Borch, Mikhail Lomonosov, and Pierre Bayen all produced oxygen in experiments in the 17th and the 18th century but none of them recognized it as a chemical element. This may have been in part due to the prevalence of the philosophy of combustion and corrosion called the phlogiston theory, which was then the favored explanation of those processes. Established in 1667 by the German alchemist J. J. Becher, one part, called phlogiston, was given off when the substance containing it was burned, while the dephlogisticated part was thought to be its true form, or calx. The fact that a substance like wood gains overall weight in burning was hidden by the buoyancy of the combustion products
9.
Sulfonic acid
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A sulfonic acid refers to a member of the class of organosulfur compounds with the general formula R−S2−OH, where R is an organic alkyl or aryl group and the S2−OH group a sulfonyl hydroxide. A sulfonic acid can be thought of as sulfuric acid with one hydroxyl group replaced by an organic substituent, the parent compound is the hypothetical compound sulfurous acid. Salts or esters of sulfonic acids are called sulfonates, a sulfonic acid is produced by the process of sulfonation. Usually the sulfonating agent is sulfur trioxide, thiols can be oxidized to sulfonic acids, RSH + 3⁄2 O2 → RSO3H Certain sulfonic acids, such as perfluorooctanesulfonic acid, are prepared by electrophilic fluorination of preformed sulfonic acids. The net conversion can be represented simplistically, C8H17SO3H +17 F2 → C8F17SO3H +17 HF Sulfonic acids are much stronger acids than the carboxylic acids. P-Toluenesulfonic acid, with a pKa of −2.8, is about a million times stronger acid than benzoic acid, similarly, methanesulfonic acid, pKa = −1.9, is also about one million times stronger acid than acetic acid. Because of their polarity, sulfonic acids tend to be crystalline solids and they are also usually colourless and nonoxidizing, which is convenient. Because of their acidity, sulfonic acids are often soluble in water or exhibit detergent-like properties. The structure of sulfonic acids is illustrated by the prototype, methanesulfonic acid, the sulfonic acid group, RSO2OH features a tetrahedral sulfur centre, meaning that sulfur is at the center of four atoms, three oxygens and one carbon. The overall geometry of the centre is reminiscent of the shape of sulfuric acid. Although both alkyl and aryl sulfonic acids are known, most of the applications are associated with the aromatic derivatives, detergents and surfactants are molecules that combine highly nonpolar and highly polar groups. Traditionally, soaps are the popular surfactants, being derived from fatty acids, since the mid-20th century, the usage of sulfonic acids has surpassed soap in advanced societies. For example, an estimated 2 billion kilograms of alkylbenzenesulfonates are produced annually for diverse purposes, lignin sulfonates, produced by sulfonation of lignin are components of drilling fluids and additives in certain kinds of concrete. Many if not most of the dyes are produced or processed via sulfonation. Sulfonic acids tend to tightly to proteins and carbohydrates. Most washable dyes are sulfonic acids for this reason, p-Cresidinesulfonic acid is used to make food dyes. Being strong acids, sulfonic acids are used as catalysts. The simplest examples are methanesulfonic acid, CH3SO2OH and p-toluenesulfonic acid, polymeric sulfonic acids are also useful
10.
Phosphorous acid
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Phosphorous acid is the compound described by the formula H3PO3. This acid is diprotic, not triprotic as might be suggested by this formula, phosphorous acid is an intermediate in the preparation of other phosphorus compounds. H3PO3 is more clearly described with the structural formula HPO2 and this species exists in equilibrium with a minor tautomer P3. IUPAC recommendations,2005, are that the latter be called phosphorous acid, only the reduced phosphorus compounds are spelled with an ous ending. The P3 tautomer has been observed as a ligand bonded to molybdenum, other important oxyacids of phosphorus are phosphoric acid and hypophosphorous acid. The reduced phosphorus acids are subject to similar tautomerism involving shifts of H between O and P, in the solid state, HP2 is tetrahedral with one shorter P=O bond of 148 pm and two longer P–O bonds of 154 pm. The central phosphorus atom is assigned a state of +3. HPO2 is the product of the hydrolysis of its acid anhydride, by concentrating the solution and precipitations with alcohols, the pure acid can be separated from the salt. Phosphorous acid is an acid with a pKa in the range 1. 26–1.3. The hydrogen bonded directly to the atom is not readily ionizable. Chemistry examinations often test students appreciation of the fact that not all three atoms are acidic under aqueous conditions, in contrast with H3PO4. Both phosphorous acid and its forms are good reducing agents. They are oxidized to phosphoric acid or its salts and it reduces solutions of noble metal cations to the metals. Phosphorous acid is used for preparing phosphite salts, such as potassium phosphite. These salts, as well as solutions of pure phosphorous acid, are fungicides. Phosphorous acid and its salts, unlike phosphoric acid, are somewhat toxic, the IUPAC name is phosphonic acid. This nomenclature is commonly reserved for substituted derivatives, that is, organic group bonded to phosphorus, for example, PO2 is methylphosphonic acid, which may of course form methylphosphonate esters. Phosphorus, An Outline of its Chemistry, Biochemistry, and Technology
11.
Double bond
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A double bond in chemistry is a chemical bond between two chemical elements involving four bonding electrons instead of the usual two. The most common double bond, that is two carbon atoms, can be found in alkenes. Many types of double bonds exist between two different elements, for example, in a carbonyl group with a carbon atom and an oxygen atom. Other common double bonds are found in azo compounds, imines and sulfoxides, in skeletal formula the double bond is drawn as two parallel lines between the two connected atoms, typographically, the equals sign is used for this. Double bonds were first introduced in chemical notation by prominent Russian chemist Alexander Butlerov, double bonds involving carbon are stronger than single bonds and are also shorter. Double bonds are also electron-rich, which makes them reactive, the type of bonding can be explained in terms of orbital hybridization. In ethylene each carbon atom has three sp2 orbitals and one p-orbital, the three sp2 orbitals lie in a plane with ~120° angles. The p-orbital is perpendicular to this plane, when the carbon atoms approach each other, two of the sp2 orbitals overlap to form a sigma bond. At the same time, the two p-orbitals approach and together form a pi-bond. For maximum overlap, the p-orbitals have to parallel, and, therefore. This property gives rise to cis-trans isomerism, double bonds are shorter than single bonds because p-orbital overlap is maximized. With 133 pm, the ethylene C=C bond length is shorter than the C−C length in ethane with 154 pm. The double bond is stronger,636 kJ mol−1 versus 368 kJ mol−1. In an alternative representation, the double bond results from two overlapping sp3 orbitals as in a bent bond, in molecules, with alternating double bonds and single bonds, p-orbital overlap can exist over multiple atoms in a chain, giving rise to a conjugated system. Conjugation can be found in such as dienes and enones. In cyclic molecules, conjugation can lead to aromaticity, in cumulenes, two double bonds are adjacent. Double bonds are common for period 2 elements carbon, nitrogen, and oxygen, metals, too, can engage in multiple bonding in a metal ligand multiple bond. Double bonded compounds, alkene homologs, R2E=ER2 are now known for all of the heavier group 14 elements, unlike the alkenes these compounds are not planar but adopt twisted and/or trans bent structures
12.
Acetyl chloride
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Acetyl chloride, CH3COCl is an acid chloride derived from acetic acid. It belongs to the class of compounds called acyl halides. It is a colorless, corrosive, volatile liquid, acetyl chloride was first prepared in 1852 by French chemist Charles Gerhardt by reacting potassium acetate with phosphoryl chloride. However, these methods usually gives acetyl chloride contaminated by phosphorus or sulfur impurities, a route avoiding these impurities of phosphorus and sulphur is that of phosgene and acetic acid, COCl2 + CH3COOH = CH3COCl + HCl + CO2. HCl impurities can be removed by distilling the product from dimethylaniline or by degassing the mixture by a stream of argon. When heated, a mixture of acid and acetic acid gives acetyl chloride. It can also be synthesized from the catalytic carbonylation of methyl chloride, acetyl chloride is not expected to exist in nature, because contact with water would hydrolyze it into acetic acid and hydrogen chloride. In fact, if handled in air it releases white smoke resulting from hydrolysis due to the moisture in the air. The smoke is actually small droplets of hydrochloric acid and acetic acid formed by hydrolysis, acetyl chloride is used for acetylation reactions, i. e. the introduction of an acetyl group. Acetyl is a group having the formula-C-CH3. For further information on the types of chemical compounds such as acetyl chloride can undergo. Two major classes of acetylations include esterification and the Friedel-Crafts reaction, acetyl chloride is a reagent for the preparation of esters and amides of acetic acid, used in the derivatization of alcohols and amines. One class of reactions are esterification. Such reactions will often proceed via ketene, a second major class of acetylation reactions are the Friedel-Crafts reactions
13.
Benzoyl chloride
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Benzoyl chloride, also known as benzenecarbonyl chloride, is an organochlorine compound with the formula C6H5COCl. It is a colourless, fuming liquid with an irritating odour and it is mainly useful for the production of peroxides but is generally useful in other areas such as in the preparation of dyes, perfumes, pharmaceuticals, and resins. It was first prepared by treatment of benzaldehyde with chlorine, an early method for production of benzoyl chloride involved chlorination of benzyl alcohol. It reacts with water to produce hydrochloric acid and benzoic acid and it reacts with alcohols to give the corresponding esters. Similarly, it reacts with amines to give the amide and it undergoes the Friedel-Crafts acylation with aromatic compounds to give the corresponding benzophenones and related derivatives. With carbanions, it again as a source of PhCO+
14.
Reagent
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A reagent /riˈeɪdʒənt/ is a substance or compound added to a system to cause a chemical reaction, or added to test if a reaction occurs. The terms reactant and reagent are often used interchangeably—however, a reactant is more specifically a substance consumed in the course of a chemical reaction, solvents, though involved in the reaction, are usually not called reactants. Similarly, catalysts are not consumed by the reaction, so they are not reactants, in biochemistry, especially in connection with enzyme-catalyzed reactions, the reactants are commonly called substrates. In organic chemistry, the term reagent denotes a chemical ingredient introduced to cause a transformation of an organic substance. Examples include the Collins reagent, Fentons reagent, and Grignard reagents, examples include Fehlings reagent, Millons reagent, and Tollens reagent. Purity standards for reagents are set by such as ASTM International or the American Chemical Society. For instance, reagent-quality water must have low levels of impurities such as sodium and chloride ions, silica. Laboratory products which are pure, but still useful and economical for undemanding work, may be designated as technical, practical. In the field of biology, the revolution in the 1980s grew from the development of reagents that could be used to identify and manipulate the chemical matter in. These reagents included antibodies, oligomers, all sorts of organisms and immortalised cell lines, reagents and methods for molecular cloning and DNA replication
15.
Amide
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An amide, also known as an acid amide, is a compound with the functional group RnExNR′2. Most common are carboxamides, but many other important types of amides are known, the term amide refers both to classes of compounds and to the functional group within those compounds. Amide can also refer to the base of ammonia or of an organic amine. For discussion of these anionic amides, see Alkali metal amides, the remainder of this article is about the carbonyl–nitrogen sense of amide. The simplest amides are derivatives of ammonia wherein one hydrogen atom has replaced by an acyl group. The ensemble is represented as RCNH2 and is described as a primary amide. Closely related and even more numerous are secondary amides which can be derived from amines and have the formula RCNHR′. Tertiary amides are commonly derived from amines and have the general structure RCNR′R″. Amides are usually regarded as derivatives of carboxylic acids in which the group has been replaced by an amine or ammonia. The lone pair of electrons on the nitrogen is delocalized into the carbonyl, consequently, the nitrogen in amides is not pyramidal. It is estimated that acetamide is described by resonance structure A for 62%, in the usual nomenclature, one adds the term amide to the stem of the parent acids name. For instance, the derived from acetic acid is named acetamide. IUPAC recommends ethanamide, but this and related names are rarely encountered. When the amide is derived from a primary or secondary amine, thus, the amide formed from dimethylamine and acetic acid is N, N-dimethylacetamide. Usually even this name is simplified to dimethylacetamide, cyclic amides are called lactams, they are necessarily secondary or tertiary amides. Functional groups consisting of –PNR2 and –SO2NR2 are phosphonamides and sulfonamides, some chemists make a pronunciation distinction between the two, saying /əˈmiːd/ for the carbonyl–nitrogen compound and /ˈeɪmaɪd/ for the anion. Others replace one of these with /ˈæmᵻd/, while others pronounce both /ˈæmᵻd/, making them homonyms. Compared to amines, amides are very weak bases, while the conjugate acid of an amine has a pKa of about 9.5, the conjugate acid of an amide has a pKa around −0.5
16.
Ester
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In chemistry, esters are chemical compounds derived from an acid in which at least one –OH group is replaced by an –O–alkyl group. Usually, esters are derived from an acid and an alcohol. Glycerides, which are fatty acid esters of glycerol, are important esters in biology, being one of the classes of lipids. Esters with low weight are commonly used as fragrances and found in essential oils. Phosphoesters form the backbone of DNA molecules, nitrate esters, such as nitroglycerin, are known for their explosive properties, while polyesters are important plastics, with monomers linked by ester moieties. The word ester was coined in 1848 by German chemist Leopold Gmelin, probably as a contraction of the German Essigäther, ester names are derived from the parent alcohol and the parent acid, where the latter may be organic or inorganic. Esters derived from more complex carboxylic acids are, on the hand, more frequently named using the systematic IUPAC name. For example, the ester hexyl octanoate, also known under the trivial name hexyl caprylate, has the formula CH36CO25CH3, the chemical formulas of organic esters usually take the form RCO2R′, where R and R′ are the hydrocarbon parts of the carboxylic acid and the alcohol, respectively. For example, butyl acetate, derived from butanol and acetic acid would be written CH3CO2C4H9, alternative presentations are common including BuOAc and CH3COOC4H9. Cyclic esters are called lactones, regardless of whether they are derived from an organic or an inorganic acid, one example of a lactone is γ-valerolactone. An uncommon class of organic esters are the orthoesters, which have the formula RC3, triethylorthoformate is derived, in terms of its name from orthoformic acid and ethanol. Esters can also be derived from an acid and an alcohol. For example, triphenyl phosphate is the derived from phosphoric acid. Organic carbonates are derived from acid, for example, ethylene carbonate is derived from carbonic acid. So far an alcohol and inorganic acid are linked via oxygen atoms, in corollary, boron features borinic esters, boronic esters, and borates. As oxygen is a group 16 chemical element, sulfur atoms can replace some oxygen atoms in carbon–oxygen–central inorganic atom covalent bonds of an ester, esters contain a carbonyl center, which gives rise to 120 ° C–C–O and O–C–O angles. Unlike amides, esters are structurally flexible functional groups because rotation about the C–O–C bonds has a low barrier and their flexibility and low polarity is manifested in their physical properties, they tend to be less rigid and more volatile than the corresponding amides. The pKa of the alpha-hydrogens on esters is around 25, the preference for the Z conformation is influenced by the nature of the substituents and solvent, if present
17.
Ion
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An ion is an atom or a molecule in which the total number of electrons is not equal to the total number of protons, giving the atom or molecule a net positive or negative electrical charge. Ions can be created, by chemical or physical means. In chemical terms, if an atom loses one or more electrons. If an atom gains electrons, it has a net charge and is known as an anion. Ions consisting of only a single atom are atomic or monatomic ions, because of their electric charges, cations and anions attract each other and readily form ionic compounds, such as salts. In the case of ionization of a medium, such as a gas, which are known as ion pairs are created by ion impact, and each pair consists of a free electron. The word ion comes from the Greek word ἰόν, ion, going and this term was introduced by English physicist and chemist Michael Faraday in 1834 for the then-unknown species that goes from one electrode to the other through an aqueous medium. Faraday also introduced the words anion for a charged ion. In Faradays nomenclature, cations were named because they were attracted to the cathode in a galvanic device, arrhenius explanation was that in forming a solution, the salt dissociates into Faradays ions. Arrhenius proposed that ions formed even in the absence of an electric current, ions in their gas-like state are highly reactive, and do not occur in large amounts on Earth, except in flames, lightning, electrical sparks, and other plasmas. These gas-like ions rapidly interact with ions of charge to give neutral molecules or ionic salts. These stabilized species are commonly found in the environment at low temperatures. A common example is the present in seawater, which are derived from the dissolved salts. Electrons, due to their mass and thus larger space-filling properties as matter waves, determine the size of atoms. Thus, anions are larger than the parent molecule or atom, as the excess electron repel each other, as such, in general, cations are smaller than the corresponding parent atom or molecule due to the smaller size of its electron cloud. One particular cation contains no electrons, and thus consists of a single proton - very much smaller than the parent hydrogen atom. Since the electric charge on a proton is equal in magnitude to the charge on an electron, an anion, from the Greek word ἄνω, meaning up, is an ion with more electrons than protons, giving it a net negative charge. A cation, from the Greek word κατά, meaning down, is an ion with fewer electrons than protons, there are additional names used for ions with multiple charges
18.
Organic reaction
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Organic reactions are chemical reactions involving organic compounds. In organic synthesis, organic reactions are used in the construction of new organic molecules, the production of many man-made chemicals such as drugs, plastics, food additives, fabrics depend on organic reactions. The oldest organic reactions are combustion of fuels and saponification of fats to make soap. Modern organic chemistry starts with the Wöhler synthesis in 1828, Organic chemistry has a strong tradition of naming a specific reaction to its inventor or inventors and a long list of so-called named reactions exists, conservatively estimated at 1000. A very old named reaction is the Claisen rearrangement and a recent named reaction is the Bingel reaction, when the named reaction is difficult to pronounce or very long as in the Corey-House-Posner-Whitesides reaction it helps to use the abbreviation as in the CBS reduction. The number of reactions hinting at the process taking place is much smaller. Another approach to organic reactions is by type of organic reagent, many of them inorganic, the major types are oxidizing agents such as osmium tetroxide, reducing agents such as Lithium aluminium hydride, bases such as lithium diisopropylamide and acids such as sulfuric acid. Factors governing organic reactions are essentially the same as that of any chemical reaction, an organic compound may consist of many isomers. Selectivity in terms of regioselectivity, diastereoselectivity and enantioselectivity is therefore an important criterion for organic reactions. The stereochemistry of pericyclic reactions is governed by the Woodward–Hoffmann rules, Organic reactions are important in the production of pharmaceuticals. There is no limit to the number of organic reactions. However, certain patterns are observed that can be used to describe many common or useful reactions. Each reaction has a reaction mechanism that explains how it happens. Organic reactions can be organized into basic types. Some reactions fit into more than one category, for example, some substitution reactions follow an addition-elimination pathway. This overview isnt intended to include every single organic reaction, rather, it is intended to cover the basic reactions. In condensation reactions a small molecule, usually water, is split off when two reactants combine in a chemical reaction, the opposite reaction, when water is consumed in a reaction, is called hydrolysis. Many Polymerization reactions are derived from organic reactions and they are divided into addition polymerizations and step-growth polymerizations
19.
Acyl halide
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An acyl halide is a chemical compound derived from an oxoacid by replacing a hydroxyl group with a halide group. If the acid is an acid, the compound contains a –COX functional group. The general formula for such an acyl halide can be written RCOX, where R may be, for example, a group, CO is the carbonyl group. Acyl chlorides are the most commonly encountered acyl halides, but acetyl iodide is the one produced on the largest scale, billions of kilograms are generated annually in the production of acetic acid. The hydroxyl group of a sulfonic acid may also be replaced by a halogen to produce the corresponding sulfonyl halide, in practical terms this is almost always chloride to give the sulfonyl chloride. Aromatic acyl halides can be prepared in similar reactions with similar reagents, however, for example, chloroformylation, a specific type of Friedel-Crafts acylation which uses formaldehyde as a reagent, or by the direct chlorination of benzaldehyde derivatives. Acyl halides are rather reactive compounds often synthesized to be used as intermediates in the synthesis of organic compounds. For example, an acyl halide can react with, water and this hydrolysis is the most heavily exploited reaction for acyl halides as it occurs in the industrial synthesis of acetic acid. An alcohol to form an ester an amine to form an amide an aromatic compound, using a Lewis acid catalyst such as AlCl3, carboxylic acids to form an organic acid anhydrides. In the above reactions, HX is also formed, for example, if the acyl halide is an acyl chloride, HCl is also formed. A molecule can have more than one acyl halide functional group, for example, adipoyl dichloride, usually simply called adipoyl chloride, has two acyl chloride functional groups, see the structure at right. It is the dichloride of the 6-carbon dicarboxylic acid adipic acid, an important use of adipoyl chloride is polymerization with an organic di-amino compound to form a polyamide called nylon or polymerization with certain other organic compounds to form polyesters. Phosgene is a toxic gas that is the dichloride of carbonic acid. Both chloride radicals in phosgene can undergo reactions analogous to the reactions of acyl halides. Phosgene is used a reactant in the production of polycarbonate polymers, volatile acyl halides are lachrymatory because they can react with water at the surface of the eye producing hydrohalic and organic acids irritating to the eye. Similar problems can result if one inhales acyl halide vapors, in general, acyl halides are irritants to the eyes, skin and mucous membranes
20.
Mass spectrum
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A mass spectrum is an intensity vs. m/z plot representing a chemical analysis. Hence, the spectrum of a sample is a pattern representing the distribution of ions by mass in a sample. It is a histogram usually acquired using an instrument called a mass spectrometer, not all mass spectra of a given substance are the same. For example, some mass spectrometers break the analyte molecules into fragments, common fragmentation processes for organic molecules are the McLafferty rearrangement and alpha cleavage. Straight chain alkanes and alkyl groups produce a series of peaks,29,43,57,71 etc. The x-axis of a mass spectrum represents a relationship between the mass of an ion and the number of elementary charges that it carries. This is written as the IUPAC standard m/z to denote the quantity formed by dividing the mass of an ion by the atomic mass unit. This has been referred to as a ratio, although in some ways it does not fit this description. The IUPAC Gold Book gives an example, for the ion C7H72+, there are several alternatives to the standard m/z notation that appear in the literature, however, these are not currently accepted by standards organizations and most journals. M/e appears in historical literature. A label more consistent with the IUPAC green book and ISO31 conventions is m/Q or m/q where m is the symbol for mass and this notation is not uncommon in the physics of mass spectrometry but is rarely used as the abscissa of a mass spectrum. It was also suggested to introduce a new unit thomson as a unit of m/z, according to this convention, mass spectra x axis could be labeled m/z and negative ions would have negative values. This notation is rare and not accepted by IUPAC or any other standards organisation, in 1897 the mass-to-charge ratio m / e of the electron was first measured by J. J. Thomson. In 1913 he measured the ratio of ions with an instrument he called a parabola spectrograph. Although this data was not represented as a mass spectrum. Eventually there was a change to the notation as m/e giving way to the current standard of m/z, early in mass spectrometry research the resolution of mass spectrometers did not allow for accurate mass determination. Francis William Aston won the Nobel prize in Chemistry in 1922, for his discovery, by means of his mass spectrograph, of isotopes, in a large number of non-radioactive elements, and for his enunciation of the Whole Number Rule. In which he stated that all atoms follow a whole-number rule This implied that the masses of atoms were not on a scale, there have been several suggestions to change the official mass spectrometry nomenclature m / z to be more internally consistent
21.
Ketone
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In chemistry, a ketone /ˈkiːtoʊn/ is an organic compound with the structure RCR, where R and R can be a variety of carbon-containing substituents. Ketones and aldehydes are simple compounds that contain a carbonyl group and they are considered simple because they do not have reactive groups like −OH or −Cl attached directly to the carbon atom in the carbonyl group, as in carboxylic acids containing −COOH. Many ketones are known and many are of importance in industry. Examples include many sugars and the industrial solvent acetone, which is the smallest ketone, the word ketone is derived from Aketon, an old German word for acetone. According to the rules of IUPAC nomenclature, ketones are named by changing the suffix -ane of the parent alkane to -anone, the position of the carbonyl group is usually denoted by a number. For the most important ketones, however, traditional names are still generally used. The common names of ketones are obtained by writing separately the names of the two alkyl groups attached to the group, followed by ketone as a separate word. The names of the groups are written alphabetically. When the two groups are the same, the prefix di- is added before the name of alkyl group. The positions of other groups are indicated by Greek letters, the α-carbon being the adjacent to carbonyl group. If both alkyl groups in a ketone are the same then the ketone is said to be symmetrical, although used infrequently, oxo is the IUPAC nomenclature for a ketone functional group. Other prefixes, however, are also used, for some common chemicals, keto or oxo refer to the ketone functional group. The term oxo is used widely through chemistry, for example, it also refers to an oxygen atom bonded to a transition metal. The ketone carbon is often described as sp2 hybridized, a description that includes both their electronic and molecular structure, ketones are trigonal planar around the ketonic carbon, with C−C−O and C−C−C bond angles of approximately 120°. Ketones differ from aldehydes in that the group is bonded to two carbons within a carbon skeleton. In aldehydes, the carbonyl is bonded to one carbon and one hydrogen and are located at the ends of carbon chains, ketones are also distinct from other carbonyl-containing functional groups, such as carboxylic acids, esters and amides. The carbonyl group is polar because the electronegativity of the oxygen is greater than that for carbon, thus, ketones are nucleophilic at oxygen and electrophilic at carbon. Because the carbonyl group interacts with water by bonding, ketones are typically more soluble in water than the related methylene compounds
22.
Dithiane
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A dithiane is a heterocyclic compound composed of a cyclohexane core structure wherein two methylene bridges are replaced by sulfur centres. The three isomeric parent heterocycles are 1, 2-dithiane,1, 3-dithiane and 1, 4-dithiane,1, 3-Dithianes are protecting group of some carbonyl-containing compounds due to their inertness to many conditions. They form by treatment of the compound with 1, 3-propanedithiol under conditions that remove water from the system. The protecting group can be removed with mercuric reagents, a process that exploits the affinity of Hg for thiolates
23.
Biochemistry
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Biochemistry, sometimes called biological chemistry, is the study of chemical processes within and relating to living organisms. By controlling information flow through biochemical signaling and the flow of energy through metabolism. Biochemistry is closely related to biology, the study of the molecular mechanisms by which genetic information encoded in DNA is able to result in the processes of life. Depending on the definition of the terms used, molecular biology can be thought of as a branch of biochemistry, or biochemistry as a tool with which to investigate. The chemistry of the cell depends on the reactions of smaller molecules. These can be inorganic, for water and metal ions, or organic, for example the amino acids. The mechanisms by which cells harness energy from their environment via chemical reactions are known as metabolism, the findings of biochemistry are applied primarily in medicine, nutrition, and agriculture. In medicine, biochemists investigate the causes and cures of diseases, in nutrition, they study how to maintain health and study the effects of nutritional deficiencies. In agriculture, biochemists investigate soil and fertilizers, and try to discover ways to improve crop cultivation, crop storage and pest control. However, biochemistry as a scientific discipline has its beginning sometime in the 19th century, or a little earlier. Gowland Hopkins on enzymes and the nature of biochemistry. The term biochemistry itself is derived from a combination of biology, the German chemist Carl Neuberg however is often cited to have coined the word in 1903, while some credited it to Franz Hofmeister. Then, in 1828, Friedrich Wöhler published a paper on the synthesis of urea and these techniques allowed for the discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as glycolysis and the Krebs cycle. Another significant historic event in biochemistry is the discovery of the gene and this part of biochemistry is often called molecular biology. In the 1950s, James D. Watson, Francis Crick, Rosalind Franklin, in 1958, George Beadle and Edward Tatum received the Nobel Prize for work in fungi showing that one gene produces one enzyme. In 1988, Colin Pitchfork was the first person convicted of murder with DNA evidence, mello received the 2006 Nobel Prize for discovering the role of RNA interference, in the silencing of gene expression. Around two dozen of the 92 naturally occurring elements are essential to various kinds of biological life. Most rare elements on Earth are not needed by life, while a few common ones are not used, most organisms share element needs, but there are a few differences between plants and animals
24.
Acyl-CoA
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Acyl-CoA is a group of coenzymes involved in the metabolism of fatty acids. It is a compound formed when coenzyme A attaches to the end of a long-chain fatty acid inside living cells. The compound undergoes beta oxidation, forming one or more molecules of acetyl-CoA and this, in turn, enters the citric acid cycle, eventually forming several molecules of ATP. To be oxidatively degraded, a fatty acid must first be activated in a reaction catalyzed by acyl-CoA synthetase. First, the fatty acid displaces the group of ATP. The acyladenylate product of the first step has a free energy of hydrolysis. The second step, transfer of the group to CoA. Fatty acids are activated in the cytosol, but oxidation occurs in the mitochondria, because there is no transport protein for CoA adducts, acyl groups must enter the mitochondria via a shuttle system involving the small molecule carnitine. Acetyl-CoA Beta oxidation Coenzyme A Acyl CoA dehydrogenase Fatty acid metabolism Acyl Coenzyme A at the US National Library of Medicine Medical Subject Headings
25.
Fatty acid
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In chemistry, particularly in biochemistry, a fatty acid is a carboxylic acid with a long aliphatic chain, which is either saturated or unsaturated. Most naturally occurring fatty acids have a chain of an even number of carbon atoms. Fatty acids are derived from triglycerides or phospholipids. Fatty acids are important dietary sources of fuel for animals because, many cell types can use either glucose or fatty acids for this purpose. Fatty acids that have double bonds are known as unsaturated. Fatty acids without double bonds are known as saturated and they differ in length as well. Fatty acid chains differ by length, often categorized as short to very long, short-chain fatty acids are fatty acids with aliphatic tails of five or fewer carbons. Medium-chain fatty acids are fatty acids with aliphatic tails of 6–12 carbons, long-chain fatty acids are fatty acids with aliphatic tails of 13 to 21 carbons. Very long chain fatty acids are fatty acids with aliphatic tails of 22 or more carbons, unsaturated fatty acids have one or more double bonds between carbon atoms. The two carbon atoms in the chain that are next to either side of the double bond can occur in a cis or trans configuration. Cis A cis configuration means that the two atoms adjacent to the double bond stick out on the same side of the chain. The rigidity of the double bond freezes its conformation and, in the case of the cis isomer, causes the chain to bend, the more double bonds the chain has in the cis configuration, the less flexibility it has. When a chain has many cis bonds, it becomes quite curved in its most accessible conformations, for example, oleic acid, with one double bond, has a kink in it, whereas linoleic acid, with two double bonds, has a more pronounced bend. α-Linolenic acid, with three bonds, favors a hooked shape. Trans A trans configuration, by contrast, means that the adjacent two hydrogen atoms lie on opposite sides of the chain, as a result, they do not cause the chain to bend much, and their shape is similar to straight saturated fatty acids. In most naturally occurring unsaturated fatty acids, each bond has three n carbon atoms after it, for some n, and all are cis bonds. Most fatty acids in the configuration are not found in nature and are the result of human processing. Fatty acids that are required by the body but cannot be made in sufficient quantity from other substrates
26.
Thioester
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In chemistry thioesters are compounds with the functional group R–S–CO–R. They are the product of esterification between an acid and a thiol. In biochemistry, the best-known thioesters are derivatives of coenzyme A, e. g. acetyl-CoA, for example, thioacetate esters are commonly prepared by alkylation of potassium thioacetate, CH3COSK + RX → CH3COSR + KCl The analogous alkylation of an acetate salt is rarely practiced. Acid anhydrides and some also give thioesters upon treatment with thiols in the presence of a base. Thioesters can be prepared from alcohols by the Mitsunobu reaction. They also arise via carbonylation of alkynes and alkenes in the presence of thiols, the carbonyl center in thioesters is reactive toward nucleophiles, even water. A reaction unique to thioesters is the Fukuyama coupling, in which the thioester is coupled with an organozinc halide by a palladium catalyst to give a ketone, the C-H groups adjacent to the carbonyl in thioesters are mildly acidic and undergo aldol condensations. This kind of reaction occurs in the biosynthesis of fatty acids, thioesters are common intermediates in many biosynthetic reactions, including the formation and degradation of fatty acids and mevalonate, precursor to steroids. Examples include malonyl-CoA, acetoacetyl-CoA, propionyl-CoA, and cinnamoyl-CoA, acetogenesis proceeds via the formation of acetyl-CoA. The biosynthesis of lignin, which comprises a fraction of the Earths land biomass. These thioesters arise analogously to those prepared synthetically, the difference being that the agent is ATP. In addition, thioesters play an important role in the tagging of proteins with ubiquitin, oxidation of the sulfur atom in thioesters is postulated in the bioactivation of the antithrombotic prodrugs ticlopidine, clopidogrel, and prasugrel. As posited in a Thioester World, thioesters are possible precursors to life, as de Duve explains, It is revealing that thioesters are obligatory intermediates in several key processes in which ATP is either used or regenerated. Thioesters are involved in the synthesis of all esters, including those found in complex lipids and they also participate in the synthesis of a number of other cellular components, including peptides, fatty acids, sterols, terpenes, porphyrins, and others. In addition, thioesters are formed as key intermediates in several particularly ancient processes that result in the assembly of ATP, in both these instances, the thioester is closer than ATP to the process that uses or yields energy. In other words, thioesters could have played the role of ATP in a thioester world initially devoid of ATP. Eventually, thioesters could have served to usher in ATP through its ability to support the formation of bonds between phosphate groups, in a thionoester, sulfur replaces the carbonyl oxygen in an ester. Such compounds are prepared by the reaction of the thioacyl chloride with an alcohol
27.
Amino acid
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Amino acids are organic compounds containing amine and carboxyl functional groups, along with a side chain specific to each amino acid. The key elements of an acid are carbon, hydrogen, oxygen. About 500 amino acids are known and can be classified in many ways, in the form of proteins, amino acids comprise the second-largest component of human muscles, cells and other tissues. Outside proteins, amino acids perform critical roles in such as neurotransmitter transport. In biochemistry, amino acids having both the amine and the acid groups attached to the first carbon atom have particular importance. They are known as 2-, alpha-, or α-amino acids and they include the 22 proteinogenic amino acids, which combine into peptide chains to form the building-blocks of a vast array of proteins. These are all L-stereoisomers, although a few D-amino acids occur in bacterial envelopes, as a neuromodulator, twenty of the proteinogenic amino acids are encoded directly by triplet codons in the genetic code and are known as standard amino acids. The other two are selenocysteine, and pyrrolysine, pyrrolysine and selenocysteine are encoded via variant codons, for example, selenocysteine is encoded by stop codon and SECIS element. N-formylmethionine is generally considered as a form of methionine rather than as a separate proteinogenic amino acid, codon–tRNA combinations not found in nature can also be used to expand the genetic code and create novel proteins known as alloproteins incorporating non-proteinogenic amino acids. Many important proteinogenic and non-proteinogenic amino acids also play critical roles within the body. Nine proteinogenic amino acids are called essential for humans because they cannot be created from other compounds by the human body, others may be conditionally essential for certain ages or medical conditions. Essential amino acids may also differ between species, because of their biological significance, amino acids are important in nutrition and are commonly used in nutritional supplements, fertilizers, and food technology. Industrial uses include the production of drugs, biodegradable plastics, the first few amino acids were discovered in the early 19th century. In 1806, French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound in asparagus that was subsequently named asparagine, cystine was discovered in 1810, although its monomer, cysteine, remained undiscovered until 1884. Glycine and leucine were discovered in 1820, usage of the term amino acid in the English language is from 1898. Proteins were found to yield amino acids after enzymatic digestion or acid hydrolysis, in the structure shown at the top of the page, R represents a side chain specific to each amino acid. The carbon atom next to the group is called the α–carbon. Amino acids containing an amino group bonded directly to the alpha carbon are referred to as amino acids
28.
Glycine
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Glycine is the amino acid that has a single hydrogen atom as its side chain. It is the simplest possible amino acid, the chemical formula of glycine is NH2‐CH2‐COOH. Glycine is one of the amino acids. Its codons are GGU, GGC, GGA, GGG of the genetic code, Glycine is a colorless, sweet-tasting crystalline solid. It is unique among the amino acids in that it is achiral. It can fit into hydrophilic or hydrophobic environments since it exists as zwitterion at natural pH, Glycine was first isolated from gelatin in 1820. The name comes from the ancient Greek word γλυκύς sweet tasting, Glycine was discovered in 1820, by Henri Braconnot who boiled a gelatinous object with sulfuric acid. Glycine is manufactured industrially by treating chloroacetic acid with ammonia, ClCH2COOH +2 NH3 → H2NCH2COOH + NH4Cl About 15 million kg are produced annually in this way, in the USA and in Japan, glycine is produced via the Strecker amino acid synthesis. Glycine is also cogenerated as an impurity in the synthesis of EDTA, arising from reactions of the ammonia coproduct. In aqueous solution, glycine itself is amphoteric, at low pH the molecule can be protonated with a pKa of about 2.4, the nature of glycine in aqueous solution has been investigated by theoretical methods. In solution the ratio of concentrations of the two isomers is independent of both the concentration and of pH. This ratio is simply the equilibrium constant for isomerization, K = / Both isomers of glycine have been observed by microwave spectroscopy in the gas phase. The solid-state structure has been analyzed in detail and this conversion is readily reversible, CO2 + NH+4 + N5, N10-Methylene tetrahydrofolate + NADH + H+ → Glycine + tetrahydrofolate + NAD+ Glycine is coded by codons GGU, GGC, GGA and GGG. Most proteins incorporate only small quantities of glycine, a notable exception is collagen, which contains about 35% glycine. Glycine is degraded via three pathways, the first step is the reverse of glycine biosynthesis from serine with serine hydroxymethyl transferase. Serine is then converted to pyruvate by serine dehydratase, in the third pathway of glycine degradation, glycine is converted to glyoxylate by D-amino acid oxidase. Glyoxylate is then oxidized by lactate dehydrogenase to oxalate in an NAD+-dependent reaction. The half-life of glycine and its elimination from the body varies significantly based on dose, in one study, the half-life was between 0.5 and 4.0 hours
29.
Lysine
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Lysine, encoded by the codons AAA and AAG, is an α-amino acid that is used in the biosynthesis of proteins. It contains a group, an α-carboxylic acid group. It is essential in humans, meaning the body cannot synthesize it, lysine is a base, as are arginine and histidine. The ε-amino group often participates in hydrogen bonding and as a base in catalysis. The ε-amino group is attached to the carbon from the α-carbon. O-Glycosylation of hydroxylysine residues in the endoplasmic reticulum or Golgi apparatus is used to mark certain proteins for secretion from the cell, deficiencies may cause blindness, as well as many other problems due to its ubiquitous presence in proteins. As an essential amino acid, lysine is not synthesized in animals, in plants and most bacteria, it is synthesized from aspartic acid, L-aspartate is first converted to L-aspartyl-4-phosphate by aspartokinase. ATP is needed as a source for this step. β-Aspartate semialdehyde dehydrogenase converts this into β-aspartyl-4-semialdehyde, energy from NADPH is used in this conversion. 4-hydroxy-tetrahydrodipicolinate synthase adds a pyruvate group to the β-aspartyl-4-semialdehyde, and a molecule is removed. This causes cyclization and gives rise to -4-hydroxy-2,3,4 and this product is reduced to 2,3,4, 5-tetrahydrodipicolinate by 4-hydroxy-tetrahydrodipicolinate reductase. This reaction consumes an NADPH molecule and releases a water molecule. Tetrahydrodipicolinate N-acetyltransferase opens this ring and gives rise to N-succinyl-L-2-amino-6-oxoheptanedionate, two water molecules and one acyl-CoA enzyme are used in this reaction. This reaction is catalyzed by the enzyme succinyl diaminopimelate aminotransferase, a glutamic acid molecule is used in this reaction and an oxoacid is produced as a byproduct. N-succinyl-LL-2, 6-diaminoheptanedionate is converted into LL-2, 6-diaminoheptanedionate by succinyl diaminopimelate desuccinylase, a water molecule is consumed in this reaction and a succinate is produced a byproduct. LL-2, 6-diaminoheptanedionate is converted by diaminopimelate epimerase into meso-2, 6-diamino-heptanedionate, finally, meso-2, 6-diamino-heptanedionate is converted into L-lysine by diaminopimelate decarboxylase. It is worth noting, however, that in fungi, euglenoids, lysine is metabolised in mammals to give acetyl-CoA, via an initial transamination with α-ketoglutarate. The bacterial degradation of lysine yields cadaverine by decarboxylation, allysine is a derivative of lysine, used in the production of elastin and collagen
30.
Ribonucleotide
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In biochemistry, a ribonucleotide or ribotide is a nucleotide containing ribose as its pentose component. It is considered a precursor of nucleic acids. Nucleotides are the building blocks of DNA and RNA. The monomer itself from ribonucleotides forms the basic building blocks for RNA, however, the reduction of ribonucleotide, by enzyme ribonucleotide reductase, forms deoxyribonucleotide, which is the essential building block for DNA. There are several differences between DNA deoxyribonucleotides and RNA ribonucleotides, successive nucleotides are linked together via phosphodiester bonds by 3-5. Ribonucleotides are also utilized in other cellular functions and these special monomers are utilized in both cell regulation and cell signaling as seen in adenosine-monophosphate. Furthermore, ribonucleotides can be converted to adenosine triphosphate, the currency in organisms. Ribonucleotides can be converted to adenosine monophosphate to regulate hormones in organisms as well. In living organisms, the most common bases for ribonucleotides are adenine, guanine, cytosine, the nitrogenous bases are classified into two parent compounds, purine and pyrimidine. The general structure of a ribonucleotide consists of a group, a ribose sugar group. Without the phosphate group, the composition of the nucleobase and sugar is known as a nucleoside, the interchangeable nitrogenous nucleobases are derived from two parent compounds, purine and pyrimidine. Nucleotides are heterocyclic compounds, that is, they contain at least two different chemical elements as members of its rings, both RNA and DNA contain two major purine bases, adenine and guanine, and two major pyrimidines. In both DNA and RNA, one of the pyrimdines is cytosine, however, DNA and RNA differ in the second major pyrimidine. DNA contains thymine while RNA contains uracil, there are some rare cases where thymine does occur in RNA and uracil in DNA. Here are the 4 major ribonucleotides which are the units of RNAs. In ribonucleotides, the component is ribose while in deoxyribonucleotides. Instead of a group at the second carbon in the ribose ring. Both types of pentoses in DNA and RNA are in their β-furanose form, DNA is defined by containing 2-deoxy-ribose nucleic acid while RNA is defined by containing ribose nucleic acid
31.
Cytidine monophosphate
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Cytidine monophosphate, also known as 5-cytidylic acid or simply cytidylate, and abbreviated CMP, is a nucleotide that is used as a monomer in RNA. It is an ester of phosphoric acid with the nucleoside cytidine, CMP consists of the phosphate group, the pentose sugar ribose, and the nucleobase cytosine, hence, a ribonucleoside monophosphate. As a substituent it takes the form of the prefix cytidylyl-, CMP can be phosphorylated to cytidine diphosphate by the enzyme CMP kinase, with adenosine triphosphate or guanosine triphosphate donating the phosphate group. Since cytidine triphosphate is generated by amination of uridine triphosphate, the source of CMP is from RNA being decomposed by RNAse
32.
Phospholipid
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Phospholipids are a class of lipids that are a major component of all cell membranes. They can form lipid bilayers because of their amphiphilic characteristic, the structure of the phospholipid molecule generally consists of two hydrophobic fatty acid tails and a hydrophilic head consisting of a phosphate group. The two components are joined together by a glycerol molecule, the phosphate groups can be modified with simple organic molecules such as choline. Biological membranes in eukaryotes also contain another class of lipid, sterol, interspersed among the phospholipids and together they provide membrane fluidity, purified phospholipids are produced commercially and have found applications in nanotechnology and materials science. An amphiphile is a term describing a chemical compound possessing both hydrophilic and lipophilic properties, the phospholipid head contains a negatively charged phosphate group and glycerol, it is hydrophilic. The phospholipid tails usually consists of 2 long fatty acid chains and these specific properties allow phospholipids to play an important role in the phospholipid bilayer. In biological systems, the phospholipids often occur with other molecules in a such as a cell membrane. Lipid bilayers occur when hydrophobic tails line up against one another, sterols contribute to membrane fluidity by hindering the packing together of phospholipids. However, this model has now superseded, as through the study of lipid polymorphism it is now known that the behaviour of lipids under physiological conditions is not simple. Liposomes are often composed of phosphatidylcholine-enriched phospholipids and may also contain mixed Phospholipid chains with surfactant properties, the ethosomal formulation of ketoconazole using phospholipids is a promising option for transdermal delivery in fungal infections. Computational simulations of phospholipids are often performed using molecular dynamics with force fields such as GROMOS, CHARMM, phospholipids are optically highly birefringent, i. e. their refractive index is different along their axis as opposed to perpendicular to it. There are no methods available for analysis of phospholipids since the close range of polarity between different phospholipid species makes detection difficult. Oil chemists often use spectroscopy to determine total Phosphorus abundance and then calculate approximate mass of phospholipids based on weight of expected fatty acid species. Modern lipid profiling employs more absolute methods of analysis, with magnetic resonance spectroscopy, particularly 31P-NMR. Phospholipid synthesis occurs in the adjacent to ER membrane that is studded with proteins that act in synthesis. Common sources of industrially produced phospholipids are soya, rapeseed, sunflower, chicken eggs, bovine milk, each source has a unique profile of individual phospholipid species and consequently differing applications in food, nutrition, pharmaceuticals, cosmetics and drug delivery. Some types of phospholipid can be split to produce products that function as second messengers in signal transduction, phospholipids also intervene in prostaglandin signal pathways as the raw material used by lipase enzymes to produce the prostaglandin precursors. In plants they serve as the raw material to produce Jasmonic acid, phospholipids can act as emulsifiers, enabling oils to form a colloid with water
33.
Phosphatidic acid
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Phosphatidic acids are the acid forms of phosphatidates, a part of common phospholipids, major constituents of cell membranes. Phosphatidic acids are the simplest diacyl-glycerophospholipids, phosphatidic acid consists of a glycerol backbone, with, in general, a saturated fatty acid bonded to carbon-1, an unsaturated fatty acid bonded to carbon-2, and a phosphate group bonded to carbon-3. Besides de novo synthesis, PA can be formed in three ways, By phospholipase D, via the hydrolysis of the P-O bond of phosphatidylcholine to produce PA and choline. By the phosphorylation of diacylglycerol by DAG kinase By the acylation of lysophosphatidic acid by lysoPA-acyltransferase, PA is degraded by conversion into DAG by lipid phosphate phosphohydrolases or into lyso-PA by phospholipase A. The role of PA in the cell can be divided into three categories, PA is the precursor for the biosynthesis of other lipids. The physical properties of PA influence membrane curvature, PA acts as a signaling lipid, recruiting cytosolic proteins to appropriate membranes. PA plays very important role in Phototransduction in Drosophila The first three roles are not mutually exclusive, PA is a vital cell lipid that acts as a biosynthetic precursor for the formation of all acylglycerol lipids in the cell. In mammalian and yeast cells, two different pathways are known for the de novo synthesis of PA, the glycerol 3-phosphate pathway or the dihydroxyacetone phosphate pathway. In bacteria, only the former pathway is present, and mutations that block this pathway are lethal, in mammalian and yeast cells, where the enzymes in these pathways are redundant, mutation of any one enzyme is not lethal. However, it is worth noting that in vitro, the various acyltransferases exhibit different substrate specificities with respect to the acyl-CoAs that are incorporated into PA. Different acyltransferases also have different intracellular distributions, such as the endoplasmic reticulum, the mitochondria or peroxisomes and this suggests that the various acyltransferases present in mammalian and yeast cells may be responsible for producing different pools of PA. The conversion of PA into diacylglycerol by LPPs is the commitment step for the production of phosphatidylcholine, phosphatidylethanolamine and phosphatidylserine, in addition, DAG is also converted into CDP-DAG, which is a precursor for phosphatidylglycerol, phosphatidylinositol and phosphoinositides. PA concentrations are maintained at low levels in the cell by the activity of potent LPPs. These convert PA into DAG very rapidly and, because DAG is the precursor for so many other lipids and this means that any upregulation in PA production can be matched, over time, with a corresponding upregulation in LPPs and in DAG metabolising enzymes. PA is, therefore, essential for synthesis and cell survival, yet. PA is a phospholipid in that it has a small highly charged head group that is very close to the glycerol backbone. PA is known to play roles in both fission and fusion, and these roles may relate to the biophysical properties of PA. At sites of membrane budding or fusion, the membrane becomes or is highly curved, a major event in the budding of vesicles, such as transport carriers from the Golgi, is the creation and subsequent narrowing of the membrane neck
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Carbohydrate
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A carbohydrate is a biological molecule consisting of carbon, hydrogen and oxygen atoms, usually with a hydrogen–oxygen atom ratio of 2,1, in other words, with the empirical formula Cmn. This formula holds true for monosaccharides, some exceptions exist, for example, deoxyribose, a sugar component of DNA, has the empirical formula C5H10O4. Carbohydrates are technically hydrates of carbon, structurally it is accurate to view them as polyhydroxy aldehydes and ketones. The term is most common in biochemistry, where it is a synonym of saccharide, a group that includes sugars, starch, the saccharides are divided into four chemical groups, monosaccharides, disaccharides, oligosaccharides, and polysaccharides. Monosaccharides and disaccharides, the smallest carbohydrates, are referred to as sugars. The word saccharide comes from the Greek word σάκχαρον, meaning sugar, while the scientific nomenclature of carbohydrates is complex, the names of the monosaccharides and disaccharides very often end in the suffix -ose. For example, grape sugar is the glucose, cane sugar is the disaccharide sucrose. Carbohydrates perform numerous roles in living organisms, polysaccharides serve for the storage of energy and as structural components. The 5-carbon monosaccharide ribose is an important component of coenzymes and the backbone of the genetic molecule known as RNA, the related deoxyribose is a component of DNA. Saccharides and their derivatives include many other important biomolecules that play key roles in the system, fertilization, preventing pathogenesis, blood clotting. In food science and in informal contexts, the term carbohydrate often means any food that is particularly rich in the complex carbohydrate starch or simple carbohydrates. Often in lists of information, such as the USDA National Nutrient Database, the term carbohydrate is used for everything other than water, protein, fat, ash. This will include chemical compounds such as acetic or lactic acid, carbohydrates are found in wide variety of foods. The important sources are cereals, potatoes, sugarcane, fruits, table sugar, bread, milk, starch and sugar are the important carbohydrates in our diet. Starch is abundant in potatoes, maize, rice and other cereals, sugar appears in our diet mainly as sucrose which is added to drinks and many prepared foods such as jam, biscuits and cakes. Glucose and fructose are found naturally in fruits and some vegetables. Glycogen is carbohydrate found in the liver and muscles, cellulose in the cell wall of all plant tissue is a carbohydrate. It is important in our diet as fibre which helps to maintain a healthy digestive system, formerly the name carbohydrate was used in chemistry for any compound with the formula Cm n
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Ligand
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In coordination chemistry, a ligand is an ion or molecule that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the electron pairs. The nature of bonding can range from covalent to ionic. Furthermore, the bond order can range from one to three. Ligands are viewed as Lewis bases, although rare cases are known to involve Lewis acidic ligand, metals and metalloids are bound to ligands in virtually all circumstances, although gaseous naked metal ions can be generated in high vacuum. Ligands in a complex dictate the reactivity of the atom, including ligand substitution rates, the reactivity of the ligands themselves. Ligand selection is a consideration in many practical areas, including bioinorganic and medicinal chemistry, homogeneous catalysis. Ligands are classified in many ways, including, charge, size, the identity of the atom. The size of a ligand is indicated by its cone angle, the composition of coordination complexes have been known since the early 1800s, such as Prussian blue and copper vitriol. The key breakthrough occurred when Alfred Werner reconciled formulas and isomers and he showed, among other things, that the formulas of many cobalt and chromium compounds can be understood if the metal has six ligands in an octahedral geometry. The first to use the term ligand were Alfred Stock and Carl Somiesky, the theory allows one to understand the difference between coordinated and ionic chloride in the cobalt ammine chlorides and to explain many of the previously inexplicable isomers. He resolved the first coordination complex called hexol into optical isomers, in general, ligands are viewed as electron donors and the metals as electron acceptors. This is because the ligand and central metal are bonded to one another, bonding is often described using the formalisms of molecular orbital theory. The HOMO can be mainly of ligands or metal character, ligands and metal ions can be ordered in many ways, one ranking system focuses on ligand hardness. Metal ions preferentially bind certain ligands, in general, soft metal ions prefer weak field ligands, whereas hard metal ions prefer strong field ligands. According to the orbital theory, the HOMO of the ligand should have an energy that overlaps with the LUMO of the metal preferential. Metal ions bound to strong-field ligands follow the Aufbau principle, whereas complexes bound to weak-field ligands follow Hunds rule. Binding of the metal with the results in a set of molecular orbitals, where the metal can be identified with a new HOMO and LUMO
36.
Fischer carbene
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A transition metal carbene complex is an organometallic compound featuring a divalent organic ligand. The divalent organic ligand coordinated to the center is called a carbene. Carbene complexes for almost all transition metals have been reported, many methods for synthesizing them and reactions utilizing them have been reported. The term carbene ligand is a formalism since many are not derived from carbenes, described often as M=CR2, they represent a class of organic ligands intermediate between alkyls and carbynes. They feature in some reactions, especially alkene metathesis, and are of value in the preparation of some fine chemicals. Metal carbene complexes are often classified into two types, the Fischer carbenes named after Ernst Otto Fischer feature strong π-acceptors at the metal and being electrophilic at the carbene carbon atom. Schrock carbenes, named after Richard R. Schrock, are characterized by more nucleophilic carbene carbon centers, n-Heterocyclic carbenes were popularlized following Arduengos isolation of a stable free carbene in 1991. Reflecting the growth of the area, carbene complexes are now known with a range of different reactivities. Often it is not possible to classify a carbene complex with regards to its electrophilicity or nucleophilicity, an example is the complex 5Cr=CPh. Fischer carbenes can be likened to ketones, with the carbene carbon being electrophilic, like ketones, Fischer carbene species can undergo aldol-like reactions. The hydrogen atoms attached to the carbon α to the carbene carbon are acidic and this carbene is the starting material for other reactions such as the Wulff-Dötz reaction. Schrock carbenes do not have π-accepting ligands and these complexes are nucleophilic at the carbene carbon atom. Schrock carbenes are typically found with, high oxidation state metal center early transition metals Ti, Ta π-donor ligands hydrogen, bonding in such complexes can be viewed as the coupling of a triplet state metal and triplet carbene. These bonds are polarized towards carbon and therefore the carbene atom is a nucleophile, an example of a Schrock carbene is the compound Ta3, with a tantalum center doubly bonded to a neopentylidene ligand as well as three neopentyl ligands. An example of interest in synthesis is Tebbes reagent. N-Heterocyclic carbenes are particularly common carbene ligands and they are popular because they are more readily prepared than Schrock and Fischer carbenes. In fact many NHCs are isolated as the ligand, since they are persistent carbenes. Being strongly stabilized by π-donating substituents, NHCs are powerful σ-donors, for this reason, the bond between the carbon and the metal center is often represented by a single dative bond, whereas Fischer and Schrock carbenes are usually depicted with double bonds to metal
37.
Methyl group
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A methyl group is an alkyl derived from methane, containing one carbon atom bonded to three hydrogen atoms — CH3. In formulas, the group is often abbreviated Me, such hydrocarbon groups occur in many organic compounds. It is a stable group in most molecules. While the methyl group is part of a larger molecule. The anion has eight electrons, the radical seven and the cation six. All three forms are highly reactive and rarely observed, the methylium cation exists in the gas phase, but is otherwise not encountered. Some compounds are considered to be sources of the CH3+ cation, the methanide anion exists only in rarefied gas phase or under exotic conditions. It can be produced by electrical discharge in ketene at low pressure, such reagents are generally prepared from the methyl halides, M + CH3X → MCH3 where M is an alkali metal. The methyl radical has the formula CH3 and it exists in dilute gases, but in more concentrated form it readily dimerizes to ethane. It can be produced by decomposition of only certain compounds. The reactivity of a methyl group depends on the adjacent substituents, methyl groups can be quite unreactive. For example, in compounds, the methyl group resists attack by even the strongest acids. The oxidation of a group occurs widely in nature and industry. The oxidation products derived from methyl are CH2OH, CHO, for example, permanganate often converts a methyl group to a carboxyl group, e. g. the conversion of toluene to benzoic acid. Ultimately oxidation of methyl groups gives protons and carbon dioxide, as seen in combustion, demethylation is a common process, and reagents that undergo this reaction are called methylating agents. Common methylating agents are dimethyl sulfate, methyl iodide, and methyl triflate, methanogenesis, the source of natural gas, arises via a demethylation reaction. Certain methyl groups can be deprotonated, for example, the acidity of the methyl groups in acetone is about 1020 more acidic than methane. The resulting carbanions are key intermediates in many reactions in organic synthesis and biosynthesis, fatty acids are produced in this way
38.
Ethyl group
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In chemistry, an ethyl group is an alkyl substituent derived from ethane. It has the formula –CH2CH3 and is often abbreviated Et. Ethylation is the formation of a compound by introduction of the ethyl group, the most widely practiced example of this reaction is the ethylation of benzene. Approximately 24.7 million tons were produced in 1999, ethylbenzene is the precursor to styrene, the precursor to polystyrene. Many ethyl-containing compounds are generated by electrophilic ethylation, i. e. treatment of nucleophiles with sources of Et+, triethyloxonium tetrafluoroborate BF4 is such a reagent. For good nucleophiles, less electrophilic reagents are employed, such as ethyl halides, in unsymmetrical ethylated compounds, the methylene protons in the ethyl substituent are diastereotopic. Chiral reagents are known to modify such substituents. The name of the group is derived from the Aether, the first-born Greek elemental god of air and hyle, the name ethyl was coined in 1835 by the Swedish chemist Jöns Jacob Berzelius
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