The RXNO Ontology is a formal ontology of chemical named reactions. [1] [2] It was originally developed at the Royal Society of Chemistry (RSC) and is associated with the Open Biomedical Ontologies Foundry. The RXNO ontology unifies several previous attempts to systematize chemical reactions including the Merck Index and the hierarchy of Carey, Laffan, Thomson and Williams. [3] [4]
The twelve top-level reaction categories proposed by Carey, Laffan, Thompson and Williams are given in the table below, together with their RXNO ontology identifiers and the equivalent Wikipedia categories where applicable. [3]
| Index | Reaction Category | RXNO ID | Wikipedia Category |
|---|---|---|---|
| 1 | Heteroatom alkylation and arylation | Category:Carbon-heteroatom bond forming reactions | |
| 2 | Acylation and related processes | ||
| 3 | Carbon-Carbon bond formation | RXNO:0000002 | Category:Carbon-carbon bond forming reactions |
| 4 | Heterocycle forming reactions | RXNO:0000349 | Category:Heterocycle forming reactions |
| 5 | Protection reactions | RXNO:0000078 | |
| 6 | Deprotection reactions | RXNO:0000203 | |
| 7 | Reductions | Category:Organic reduction reactions | |
| 8 | Oxidations | Category:Organic oxidation reactions | |
| 9 | Functional group interconversion (FGI) | RXNO:0000011 | Category:Substitution reactions |
| 10 | Functional group addition (FGA) | ||
| 11 | Resolution reactions | ||
| 12 | Miscellaneous | Category:Organic reactions |
The following table lists the RXNO identifiers for some example name reactions.
In organic chemistry, phenols, sometimes called phenolics, are a class of chemical compounds consisting of one or more hydroxyl groups (−OH) bonded directly to an aromatic hydrocarbon group. The simplest is phenol, C
6H
5OH. Phenolic compounds are classified as simple phenols or polyphenols based on the number of phenol units in the molecule.
Organic reactions are chemical reactions involving organic compounds. The basic organic chemistry reaction types are addition reactions, elimination reactions, substitution reactions, pericyclic reactions, rearrangement reactions, photochemical reactions and redox reactions. 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.
An aldol condensation is a condensation reaction in organic chemistry in which two carbonyl moieties react to form a β-hydroxyaldehyde or β-hydroxyketone, and this is then followed by dehydration to give a conjugated enone.
Medicinal or pharmaceutical chemistry is a scientific discipline at the intersection of chemistry and pharmacy involved with designing and developing pharmaceutical drugs. Medicinal chemistry involves the identification, synthesis and development of new chemical entities suitable for therapeutic use. It also includes the study of existing drugs, their biological properties, and their quantitative structure-activity relationships (QSAR).
Organic synthesis is a special branch of chemical synthesis and is concerned with the intentional construction of organic compounds. Organic molecules are often more complex than inorganic compounds, and their synthesis has developed into one of the most important branches of organic chemistry. There are several main areas of research within the general area of organic synthesis: total synthesis, semisynthesis, and methodology.
The Cope rearrangement is an extensively studied organic reaction involving the [3,3]-sigmatropic rearrangement of 1,5-dienes. It was developed by Arthur C. Cope and Elizabeth Hardy. For example, 3-methyl-hexa-1,5-diene heated to 300 °C yields hepta-1,5-diene.
Acyloin condensation is a reductive coupling of two carboxylic esters using metallic sodium to yield an α-hydroxyketone, also known as an acyloin.
The Bamford–Stevens reaction is a chemical reaction whereby treatment of tosylhydrazones with strong base gives alkenes. It is named for the British chemist William Randall Bamford and the Scottish chemist Thomas Stevens Stevens (1900–2000). The usage of aprotic solvents gives predominantly Z-alkenes, while protic solvent gives a mixture of E- and Z-alkenes. As an alkene-generating transformation, the Bamford–Stevens reaction has broad utility in synthetic methodology and complex molecule synthesis.
The Claisen rearrangement is a powerful carbon–carbon bond-forming chemical reaction discovered by Rainer Ludwig Claisen. The heating of an allyl vinyl ether will initiate a [3,3]-sigmatropic rearrangement to give a γ,δ-unsaturated carbonyl, driven by exergonically favored carbonyl CO bond formation.
The Reformatsky reaction is an organic reaction which condenses aldehydes or ketones with α-halo esters using metallic zinc to form β-hydroxy-esters:
In stereochemistry, a chiral auxiliary is a stereogenic group or unit that is temporarily incorporated into an organic compound in order to control the stereochemical outcome of the synthesis. The chirality present in the auxiliary can bias the stereoselectivity of one or more subsequent reactions. The auxiliary can then be typically recovered for future use.
Acyloins or α-hydroxy ketones are a class of organic compounds which all possess a hydroxy group adjacent to a ketone group. The name acyloin is derived from the fact that they are formally derived from reductive coupling of carboxylic acyl groups.
In organic chemistry, umpolung or polarity inversion is the chemical modification of a functional group with the aim of the reversal of polarity of that group. This modification allows secondary reactions of this functional group that would otherwise not be possible. The concept was introduced by D. Seebach and E.J. Corey. Polarity analysis during retrosynthetic analysis tells a chemist when umpolung tactics are required to synthesize a target molecule.
The Gabriel–Colman rearrangement is the chemical reaction of a saccharin or phthalimido ester with a strong base, such as an alkoxide, to form substituted isoquinolines. First described in 1900 by chemists Siegmund Gabriel and James Colman, this rearrangement, a ring expansion, is seen to be general if there is an enolizable hydrogen on the group attached to the nitrogen, since it is necessary for the nitrogen to abstract a hydrogen to form the carbanion that will close the ring. As shown in the case of the general example below, X is either CO or SO2.
The total synthesis of quinine, a naturally-occurring antimalarial drug, was developed over a 150-year period. The development of synthetic quinine is considered a milestone in organic chemistry although it has never been produced industrially as a substitute for natural occurring quinine. The subject has also been attended with some controversy: Gilbert Stork published the first stereoselective total synthesis of quinine in 2001, meanwhile shedding doubt on the earlier claim by Robert Burns Woodward and William Doering in 1944, claiming that the final steps required to convert their last synthetic intermediate, quinotoxine, into quinine would not have worked had Woodward and Doering attempted to perform the experiment. A 2001 editorial published in Chemical & Engineering News sided with Stork, but the controversy was eventually laid to rest once and for all when Williams and coworkers successfully repeated Woodward's proposed conversion of quinotoxine to quinine in 2007.
In organic chemistry, a cross-coupling reaction is a reaction where two different fragments are joined. Cross-couplings are a subset of the more general coupling reactions. Often cross-coupling reactions require metal catalysts. One important reaction type is this:
Cyclopentyl methyl ether (CPME), also known as methoxycyclopentane, is hydrophobic ether solvent. A high boiling point of 106 °C (223 °F) and preferable characteristics such as low formation of peroxides, relative stability under acidic and basic conditions, formation of azeotropes with water coupled with a narrow explosion range render CPME an attractive alternative to other ethereal solvents such as tetrahydrofuran (THF), 2-methyltetrahydrofuran (2-MeTHF), dioxane, and 1,2-dimethoxyethane (DME).
Bis(cyclopentadienyl)titanium(III) chloride, also known as the Nugent–RajanBabu reagent, is the organotitanium compound which exists as a dimer with the formula [(C5H5)2TiCl]2. It is an air sensitive green solid. The complex finds specialized use in synthetic organic chemistry as a single electron reductant.
Vy Maria Dong is a Vietnamese-American Professor of Chemistry at the University of California, Irvine (UCI). Dong works on enantioselective catalysis and natural product synthesis. She received the Royal Society of Chemistry's Merck, Sharp & Dohme Award in 2020, the American Chemical Society's Elias James Corey Award in 2019, and the UCI's Distinguished Alumni Award in 2018.