In chemistry a phosphite ester or organophosphite refers to an organophosphorous compound with the formula P3. They can be considered as esters of an unobserved tautomer phosphorous acid, H3PO3, with the simplest example being trimethylphosphite, P3; some phosphites can be considered esters of the dominant tautomer of phosphorous acid. The simplest representative is dimethylphosphite with the formula HP2. Both classes of phosphites are colorless liquids. From PCl3Phosphite esters are prepared by treating phosphorus trichloride with an alcohol. Depending on the synthetic details, this alcoholysis can give the diorganophosphites: PCl3 + 3 C2H5OH → 2PH + 2 HCl + C2H5ClAlternatively, when the alcoholysis is conducted in the presence of proton acceptors, one obtains the C3-symmetric trialkoxy derivatives: PCl3 + 3 C2H5OH + 3 R3N → 3P + 3 R3NHClNumerous derivatives have been prepared for both types of phosphites. By transesterificationPhosphite esters can be prepared by transesterification, as they undergo alcohol exchange upon heating with other alcohols.
This process can be used to produce mixed alkyl phosphites. Alternatively, if the phosphite of a volatile alcohol is used, such as trimethyl phosphite the by product can be removed by distillation, allowing the reaction to be driven to completion. Phosphites are oxidized to phosphate esters: P3 + → OP3This reaction underpins the commercial use of some phosphite esters as stabilizers in polymers. Alkyl phosphite esters are used in the Perkow reaction for the formation of vinyl phosphonates, in the Michaelis–Arbuzov reaction to form phosphonates. Aryl phosphite esters may not undergo these reactions and hence are used as stabilizers in halogen-bearing polymers such as PVC. Phosphite esters may be used as reducing agents in more specialised cases. For example, triethylphosphite is known to reduce certain hydroperoxides to alcohols formed by autoxidation. In this process the phosphite is converted to a phosphate ester; this reaction type is utilized in the Wender Taxol total synthesis. Phosphite esters hence can form coordination complexes with various metal ions.
Representative phosphite ligands include trimethylphosphite, triethylphosphite, trimethylolpropane phosphite, triphenylphosphite. In contrast to phosphine ligands, phosphites exhibit a smaller ligand cone angles, making them appealing as ligands, they remain somewhat less important. Diorganophosphites are derivatives of phosphorus and can be viewed as the di-esters of phosphorous acid, they exhibit tautomerism, however the equilibrium overwhelmingly favours the right-hand form: 2POH ⇌ 2PHThe P-H bond is the site of high reactivity in these compounds, whereas in tri-organophosphites the lone pair on phosphorus is the site of high reactivity. Diorganophosphites do however undergo transesterification. Phosphinite PR2 Phosphonite P2R Ortho ester CH3 Borate ester B3
A hemiacetal or a hemiketal is a compound that results from the addition of an alcohol to an aldehyde or a ketone, respectively. The Greek word hèmi, meaning half, refers to the fact that a single alcohol has been added to the carbonyl group, in contrast to acetals or ketals, which are formed when a second alkoxy group has been added to the structure; the general formula of a hemiacetal is R1R2COR,where R1 or R2 is hydrogen and R is not hydrogen. While in the IUPAC definition of a hemiacetal R1 or R2 may or may not be a hydrogen, in a hemiketal none of the R-groups can be a hydrogen. Hemiketals are regarded as hemiacetals where none of the R-groups are H, are therefore a subclass of the hemiacetals. Hemiacetals and hemiketals are unstable compounds. In some cases however, stable cyclic hemiacetals and hemiketals, called lactols, can be formed with 5- and 6-membered rings. In this case an intramolecular OH group reacts with the carbonyl group. Glucose and many other aldoses exist as cyclic hemiacetals whereas fructose and similar ketoses exist as cyclic hemiketals.
Hemiacetals can be synthesized in a number of ways: Nucleophilic addition of an alcohol to a carbonyl group of an aldehyde Nucleophilic addition of an alcohol to a resonance stabilized hemiacetal cation Partial hydrolysis of an acetal Hemiacetals and hemiketals may be thought of as intermediates in the reaction between alcohols and aldehydes or ketones, with the final product being an acetal or a ketal: -C=O + 2 ROH ⇌ -C + ROH ⇌ -C2 + H2OA hemiacetal can react with an alcohol under acidic conditions to form an acetal, can dissociate to form an aldehyde and an alcohol. Hemiacetal + alcohol + acid ↔ acetal + waterAn aldehyde dissolved in water exists in equilibrium with low concentrations of its hydrate, R-CH2. In excess alcohol, the aldehyde, its hemiacetal, its acetal all exist in solution. A hemiacetal results from nucleophilic attack by the alcohol's hydroxyl group on the carbon of the C=O bond. Acetals are products of substitution reactions catalyzed by acid; the presence of acid improves the leaving capacity of the hydroxyl group and enables its substitution with an alkoxyl group.
The conversion of a hemiacetal to an acetal is an SN1 reaction. Ketones give ketals; these do not form as as hemiacetals and acetals. To increase yields of ketals or acetals, water formed during the reaction can be removed, in accord with Le Châtelier's principle
Nucleobases known as nitrogenous bases or simply bases, are nitrogen-containing biological compounds that form nucleosides, which in turn are components of nucleotides, with all of these monomers constituting the basic building blocks of nucleic acids. The ability of nucleobases to form base pairs and to stack one upon another leads directly to long-chain helical structures such as ribonucleic acid and deoxyribonucleic acid. Five nucleobases—adenine, guanine and uracil —are called primary or canonical, they function as the fundamental units of the genetic code, with the bases A, G, C, T being found in DNA while A, G, C, U are found in RNA. Thymine and uracil are identical excepting. Adenine and guanine have a fused-ring skeletal structure derived of purine, hence they are called purine bases; the simple-ring structure of cytosine and thymine is derived of pyrimidine, so those three bases are called the pyrimidine bases. Each of the base pairs in a typical double-helix DNA comprises a purine and a pyrimidine: either an A paired with a T or a C paired with a G.
These purine-pyrimidine pairs, which are called base complements, connect the two strands of the helix and are compared to the rungs of a ladder. The pairing of purines and pyrimidines may result, in part, from dimensional constraints, as this combination enables a geometry of constant width for the DNA spiral helix; the A-T and C-G pairings function to form double or triple hydrogen bonds between the amine and carbonyl groups on the complementary bases. In August 2011, a report based on NASA studies of meteorites suggested that nucleobases such as adenine, xanthine, purine, 2,6-diaminopurine, 6,8-diaminopurine may have formed in outer space as well as on earth; the origin of the term base reflects these compounds' chemical properties in acid-base reactions, but those properties are not important for understanding most of the biological functions of nucleobases. At the sides of nucleic acid structure, phosphate molecules successively connect the two sugar-rings of two adjacent nucleotide monomers, thereby creating a long chain biomolecule.
These chain-joins of phosphates with sugars create the "backbone" strands for a single- or double helix biomolecule. In the double helix of DNA, the two strands are oriented chemically in opposite directions, which permits base pairing by providing complementarity between the two bases, and, essential for replication of or transcription of the encoded information found in DNA. DNA and RNA contain other bases that have been modified after the nucleic acid chain has been formed. In DNA, the most common modified base is 5-methylcytosine. In RNA, there are many modified bases, including those contained in the nucleosides pseudouridine, inosine, 7-methylguanosine. Hypoxanthine and xanthine are two of the many bases created through mutagen presence, both of them through deamination. Hypoxanthine is produced from adenine, xanthine from guanine, uracil results from deamination of cytosine; these are examples of modified guanosine. These are examples of modified thymine or uridine. A vast number of nucleobase analogues exist.
The most common applications are used as fluorescent probes, either directly or indirectly, such as aminoallyl nucleotide, which are used to label cRNA or cDNA in microarrays. Several groups are working on alternative "extra" base pairs to extend the genetic code, such as isoguanine and isocytosine or the fluorescent 2-amino-6-purine and pyrrole-2-carbaldehyde. In medicine, several nucleoside analogues are used as antiviral agents; the viral polymerase incorporates these compounds with non-canonical bases. These compounds are activated in the cells by being converted into nucleotides. At least one set of new base pairs has been announced as of May 2014. Nucleoside Nucleotide Nucleic acid notation Nucleic acid sequence Base pairing in DNA Double Helix
In chemistry, delocalized electrons are electrons in a molecule, ion or solid metal that are not associated with a single atom or a covalent bond. The term is general and can have different meanings in different fields. In organic chemistry, this refers to resonance in aromatic compounds. In solid-state physics, this refers to free electrons. In quantum chemistry, this refers to molecular orbital electrons that extend over several adjacent atoms. In the simple aromatic ring of benzene the delocalization of six π electrons over the C6 ring is graphically indicated by a circle; the fact that the six C-C bonds are equidistant is one indication that the π electrons are delocalized. In valence bond theory, delocalization in benzene is represented by resonance structures. Delocalized electrons exist in the structure of solid metals. Metallic structure consists of aligned positive ions in a "sea" of delocalized electrons; this means that the electrons are free to move throughout the structure, gives rise to properties such as conductivity.
In diamond all four outer electrons of each carbon atom are'localized' between the atoms in covalent bonding. The movement of electrons is restricted and diamond does not conduct an electric current. In graphite, each carbon atom uses only 3 of its 4 outer energy level electrons in covalently bonding to three other carbon atoms in a plane; each carbon atom contributes one electron to a delocalized system of electrons, a part of the chemical bonding. The delocalized electrons are free to move throughout the plane. For this reason, graphite conducts electricity along the planes of carbon atoms, but does not conduct in a direction at right angles to the plane. Standard ab initio quantum chemistry methods lead to delocalized orbitals that, in general, extend over an entire molecule and have the symmetry of the molecule. Localized orbitals may be found as linear combinations of the delocalized orbitals, given by an appropriate unitary transformation. In the methane molecule for example, ab initio calculations show bonding character in four molecular orbitals, sharing the electrons uniformly among all five atoms.
There are two orbital levels, a bonding molecular orbital formed from the 2s orbital on carbon and triply degenerate bonding molecular orbitals from each of the 2p orbitals on carbon. The localized sp3 orbitals corresponding to each individual bond in valence bond theory can be obtained from a linear combination of the four molecular orbitals. Aromatic ring current Electride Solvated electron
In organic chemistry, keto–enol tautomerism refers to a chemical equilibrium between a keto form and an enol. The enol and keto forms are said to be tautomers of each other; the interconversion of the two forms involves the movement of an alpha hydrogen atom and the reorganisation of bonding electrons. A compound containing a carbonyl group is in rapid equilibrium with an enol tautomer, which contains a pair of doubly bonded carbon atoms adjacent to a hydroxyl group, C=C-OH; the keto form predominates at equilibrium for most ketones. Nonetheless, the enol form is important for some reactions; the deprotonated intermediate in the interconversion of the two forms, referred to as an enolate anion, is important in carbonyl chemistry, in large part because it is a strong nucleophile. The keto–enol tautomerization chemical equilibrium is thermodynamically driven, at room temperature the equilibrium favors the formation of the keto form. A classic example for favoring the keto form can be seen in the equilibrium between vinyl alcohol and acetaldehyde.
However, it is reported that in the case of vinyl alcohol, formation of a stabilized enol form can be accomplished by controlling the water concentration in the system and utilizing the kinetic favorability of the deuterium produced kinetic isotope effect. Deuterium stabilization can be accomplished through hydrolysis of a ketene precursor in the presence of a slight stoichiometric excess of heavy water. Studies show that the tautomerization process is inhibited at ambient temperatures, the half life of the enol form can be increased to t1/2 = 42 minutes for first order hydrolysis kinetics; the acid catalyzed conversion of an enol to the keto form proceeds by a two step mechanism in an aqueous acidic solution. For this, it is necessary that the alpha carbon atom contains at least one hydrogen atom known as the alpha hydrogen atom; this alpha hydrogen atom must additionally be positioned such that it may line up parallel with the antibonding pi-orbital of the carbonyl group. The hyperconjugation of this bond with the C–H bond at the alpha carbon atom reduces the electron density of the C–H bond and weakens it, making the alpha hydrogen atom more acidic.
When the alpha hydrogen atom is not aligned with the pi orbital, for example in the adamantanone or other polycyclic ketones, the enolization is impossible or slow. In the first step of the mechanism, the exposed electrons of the C=C double bond of the enol are donated to a hydronium ion; this addition follows Markovnikov's rule, thus the proton is added to the carbon atom with more attached hydrogen atoms. This is a concerted step with the oxygen atom in the hydroxyl group donating electrons to produce the eventual carbonyl group. One of the early investigators into keto–enol tautomerism was Emil Erlenmeyer, his Erlenmeyer rule, developed in 1880, states that all alcohols in which the hydroxyl group is attached directly to a double-bonded carbon atom become aldehydes or ketones. This conversion occurs; the keto form is therefore favored at equilibrium. See also: Stereochemistry of ketonization of enols and enolatesIf R1 and R2 are different substituents, there is a new stereocenter formed at the alpha position when an enol converts to its keto form.
Depending on the nature of the three R groups, the resulting products in this situation would be diastereomers or enantiomers. In certain aromatic compounds such as phenol, the enol is important due to the aromatic character of the enol but not the keto form. Melting the naphthalene derivative naphthalene-1,4-diol, which has the 1,4-diol as part of an aromatic ring, at 200 °C results in a 2:1 mixture with the diketo form, where the ring with the oxygen atoms has become non-aromatic. Heating the diketo form in benzene at 120 °C for three days affords a mixture; the keto product reverts to the enol in presence of a base. The keto form can be obtained in a pure form by stirring the keto form in trifluoroacetic acid and toluene followed recrystallisation from isopropyl ether; when the enol form is complexed with chromium tricarbonyl, complete conversion to the keto form accelerates and occurs at room temperature in benzene. Keto–enol tautomerism is important in several areas of biochemistry; the high phosphate-transfer potential of phosphoenolpyruvate results from the fact that the phosphorylated compound is "trapped" in the less thermodynamically favorable enol form, whereas after dephosphorylation it can assume the keto form.
Rare enol tautomers of the bases guanine and thymine can lead to mutation because of their altered base-pairing properties. Keto-enol and the analogous amino-imino tautomerism are among the primary causes of spontaneous mutations during DNA replication and repair. In deoxyribonucleic acids the nucleotide bases are in the keto form, stabilized by the hydrogen bonding that holds together the two strands of the DNA double-helix. Single-stranded DNA exists transiently during replication, there a rare shift to the enol form of Thymine or Guanine can occur. If the position of the enol base is replicated before it reverts to keto configuration, the result is incorporation of a mismatched base. For example, the tautomeric shift of keto-Guanine to enol-Guanine causes it to pair with Thymine rather than its normal partner, Cytosine; the tautomeric shift is tran
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 amino acid are carbon, hydrogen and nitrogen, although other elements are found in the side chains of certain amino acids. About 500 occurring amino acids are known and can be classified in many ways, they can be classified according to the core structural functional groups' locations as alpha-, beta-, gamma- or delta- amino acids. In the form of proteins, amino acid residues form the second-largest component of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis. In biochemistry, amino acids having both the amine and the carboxylic acid groups attached to the first carbon atom have particular importance, they are known as α-amino acids. 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, in some antibiotics. 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, pyrrolysine. Pyrrolysine and selenocysteine are encoded via variant codons. N-formylmethionine is considered as a form of methionine rather than as a separate proteinogenic amino acid. Codon–tRNA combinations not found in nature can be used to "expand" the genetic code and form novel proteins known as alloproteins incorporating non-proteinogenic amino acids. Many important proteinogenic and non-proteinogenic amino acids have biological functions. For example, in the human brain and gamma-amino-butyric acid are the main excitatory and inhibitory neurotransmitters. Hydroxyproline, a major component of the connective tissue collagen, is synthesised from proline. Glycine is a biosynthetic precursor to porphyrins used in red blood cells.
Carnitine is used in lipid transport. Nine proteinogenic amino acids are called "essential" for humans because they cannot be produced from other compounds by the human body and so must be taken in as food. Others may be conditionally essential for medical conditions. Essential amino acids may differ between species; because of their biological significance, amino acids are important in nutrition and are used in nutritional supplements, fertilizers and food technology. Industrial uses include the production of drugs, biodegradable plastics, chiral catalysts; 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, subsequently named asparagine, the first amino acid to be discovered. Cystine was discovered in 1810, although its monomer, remained undiscovered until 1884. Glycine and leucine were discovered in 1820; the last of the 20 common amino acids to be discovered was threonine in 1935 by William Cumming Rose, who determined the essential amino acids and established the minimum daily requirements of all amino acids for optimal growth.
The unity of the chemical category was recognized by Wurtz in 1865, but he gave no particular name to it. Usage of the term "amino acid" in the English language is from 1898, while the German term, Aminosäure, was used earlier. Proteins were found to yield amino acids after enzymatic acid hydrolysis. In 1902, Emil Fischer and Franz Hofmeister independently proposed that proteins are formed from many amino acids, whereby bonds are formed between the amino group of one amino acid with the carboxyl group of another, resulting in a linear structure that Fischer termed "peptide". 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 carboxyl group is called the α–carbon. Amino acids containing an amino group bonded directly to the alpha carbon are referred to as alpha amino acids; these include amino acids such as proline which contain secondary amines, which used to be referred to as "imino acids". The alpha amino acids are the most common form found in nature, but only when occurring in the L-isomer.
The alpha carbon is a chiral carbon atom, with the exception of glycine which has two indistinguishable hydrogen atoms on the alpha carbon. Therefore, all alpha amino acids but glycine can exist in either of two enantiomers, called L or D amino acids, which are mirror images of each other. While L-amino acids represent all of the amino acids found in proteins during translation in the ribosome, D-amin
A proton is a subatomic particle, symbol p or p+, with a positive electric charge of +1e elementary charge and a mass less than that of a neutron. Protons and neutrons, each with masses of one atomic mass unit, are collectively referred to as "nucleons". One or more protons are present in the nucleus of every atom; the number of protons in the nucleus is the defining property of an element, is referred to as the atomic number. Since each element has a unique number of protons, each element has its own unique atomic number; the word proton is Greek for "first", this name was given to the hydrogen nucleus by Ernest Rutherford in 1920. In previous years, Rutherford had discovered that the hydrogen nucleus could be extracted from the nuclei of nitrogen by atomic collisions. Protons were therefore a candidate to be a fundamental particle, hence a building block of nitrogen and all other heavier atomic nuclei. In the modern Standard Model of particle physics, protons are hadrons, like neutrons, the other nucleon, are composed of three quarks.
Although protons were considered fundamental or elementary particles, they are now known to be composed of three valence quarks: two up quarks of charge +2/3e and one down quark of charge –1/3e. The rest masses of quarks contribute only about 1% of a proton's mass, however; the remainder of a proton's mass is due to quantum chromodynamics binding energy, which includes the kinetic energy of the quarks and the energy of the gluon fields that bind the quarks together. Because protons are not fundamental particles, they possess a physical size, though not a definite one. At sufficiently low temperatures, free protons will bind to electrons. However, the character of such bound protons does not change, they remain protons. A fast proton moving through matter will slow by interactions with electrons and nuclei, until it is captured by the electron cloud of an atom; the result is a protonated atom, a chemical compound of hydrogen. In vacuum, when free electrons are present, a sufficiently slow proton may pick up a single free electron, becoming a neutral hydrogen atom, chemically a free radical.
Such "free hydrogen atoms" tend to react chemically with many other types of atoms at sufficiently low energies. When free hydrogen atoms react with each other, they form neutral hydrogen molecules, which are the most common molecular component of molecular clouds in interstellar space. Protons are composed of three valence quarks, making them baryons; the two up quarks and one down quark of a proton are held together by the strong force, mediated by gluons. A modern perspective has a proton composed of the valence quarks, the gluons, transitory pairs of sea quarks. Protons have a positive charge distribution which decays exponentially, with a mean square radius of about 0.8 fm. Protons and neutrons are both nucleons, which may be bound together by the nuclear force to form atomic nuclei; the nucleus of the most common isotope of the hydrogen atom is a lone proton. The nuclei of the heavy hydrogen isotopes deuterium and tritium contain one proton bound to one and two neutrons, respectively. All other types of atomic nuclei are composed of two or more protons and various numbers of neutrons.
The concept of a hydrogen-like particle as a constituent of other atoms was developed over a long period. As early as 1815, William Prout proposed that all atoms are composed of hydrogen atoms, based on a simplistic interpretation of early values of atomic weights, disproved when more accurate values were measured. In 1886, Eugen Goldstein discovered canal rays and showed that they were positively charged particles produced from gases. However, since particles from different gases had different values of charge-to-mass ratio, they could not be identified with a single particle, unlike the negative electrons discovered by J. J. Thomson. Wilhelm Wien in 1898 identified the hydrogen ion as particle with highest charge-to-mass ratio in ionized gases. Following the discovery of the atomic nucleus by Ernest Rutherford in 1911, Antonius van den Broek proposed that the place of each element in the periodic table is equal to its nuclear charge; this was confirmed experimentally by Henry Moseley in 1913 using X-ray spectra.
In 1917, Rutherford proved that the hydrogen nucleus is present in other nuclei, a result described as the discovery of protons. Rutherford had earlier learned to produce hydrogen nuclei as a type of radiation produced as a product of the impact of alpha particles on nitrogen gas, recognize them by their unique penetration signature in air and their appearance in scintillation detectors; these experiments were begun when Rutherford had noticed that, when alpha particles were shot into air, his scintillation detectors showed the signatures of typical hydrogen nuclei as a product. After experimentation Rutherford traced the reaction to the nitrogen in air, found that when alphas were produced into pure nitrogen gas, the effect was larger. Rutherford determined that this hydrogen could have come only from the nitrogen, therefore nitrogen must contain hydrogen nuclei. One hydrogen nucleus was being knocked off by the impact of the alpha particle, producing oxygen-17 in the process; this was 14N + α → 17O + p.
(This reaction wo