Chemical structure IUPAC nomenclature

For many decades intramolecular O-coupling was considered not to take place in the diazotization products of 2-aminophenol and its derivatives (for a contrary opinion see, however, Kazitsyna and Klyueva, 1972). The compounds were assumed to be present as one structure only, which can be represented as a mesomer of a phenoxide diazonium zwitterion 6.63 b and a diazocyclohexadienone 6.63 a (see reviews by Kazitsyna et al., 1966 Meier and Zeller, 1977 Ershov et al., 1981). In IUPAC nomenclature 6.63 is called 1,2-quinone diazide, in Chemical Abstracts 6-diazo-2,4-cyclohexadien-one (see Sec. 1.3). More recently, however, Schulz and Schweig (1979, 1984) were able to identify the intramolecular product of O-coupling, i.e., 1,2,3-benzooxadiazole (6.64) after condensation of 6.63 in vacuo at 15 K in the presence of argon (see Sec. 4.2). 

The IUPAC rules are not the only nomenclature system in use today. Chemical Abstracts Service surveys all the world s leading scientific journals that publish papers relating to chemistry and publishes brief abstracts of those papers. The publication Chemical Abstracts and its indexes are absolutely essential to the practice of chemistry. For many years Chemical Abstracts nomenclature was very similar to IUPAC nomenclature, but the tremendous explosion of chemical knowledge has required Chemical Abstracts to modify its nomenclature so that its indexes are better adapted to computerized searching. This means that whenever feasible, a compound has a single Chemical Abstracts name. Unfortunately, this Chemical Abstracts name may be different from any of the several IUPAC names. In general, it is easier to make the mental connection between a chemical structure and its IUPAC name than its Chemical Abstracts name. 

Names like this are fine for familiar compounds that are widely used and referred to by chemists, biologists, doctors, nurses, perfumers alike. But there are over 16 million known organic compounds. They can t all have simple names, and no one would remember them if they did, For this reason, the IUPAC (International Union of Pure and Applied Chemistry) have developed systematic nomenclature, a set of rules that allows any compound to be given a unique name that can be deduced directly from its chemical structure. Conversely, a chemical structure can be deduced from its systematic name. 

A significant fraction, however, of the documents in the scientific literature dealing with chemical entities and their biological effects are not composed of trivial names for the compounds under investigation. For the automated analysis of the chemical named entities in these publications, we need to use other methods. In principle, it should be possible to use rule-based approaches to identify IUPAC names (and other forms of IUPAC-like expressions), in particular, because the IUPAC name construction itself is based on rules. However, IUPAC names are neither unambiguous, nor can they easily be checked automatically for compliance with IUPAC nomenclature rules. In fact, most IUPAC-like expressions in patent literature seem to be not compliant with the IUPAC nomenclature, and cannot easily be converted into structures.40... 

IUPAC-like expressions, true IUPAC nomenclature names, and InChl and SMILES representations of chemical compounds are well suited for detection by machine learning approaches. Conditional random fields (CRFs)41 and support vector machines have been used for the detection of IUPAC expressions in scientific literature 42 Other approaches are based on rules sets43 44 or combinations of machine learning with rule-based approaches 45 All these approaches have in common that they face one significant problem the name-to-structure problem. 

Chemical compound entity extraction is a different type of entity extraction. One cannot refer to a complete dictionary or thesaurus of chemical compound names, as there is practically an infinite number of compound names. Systematic names, such as the International Union of Pure and Applied Chemistry (IUPAC) nomenclature system [54], are created from a set of rules that determine the name of a chemical compound based on the chemical structure. As an example we show aspirin, which has the common chemical name acetyl salicylic acid and the IUPAC name 2-acetyloxybenzoic acid. The common names, including aspirin, can be found using a thesaurus-based approach with low levels of ambiguity. The IUPAC name is a systematically determined name that must be tagged in the text using a heuristics-based approach (rules based). In many cases, one will have only the IUPAC name, not a known common name, for a compound. 

The 2008 lUPAC Recommendations Graphical Representation Standards for Chemical Structure Diagrams can be accessed at http //www.iupac. org/publications/pac/80/2/027 7/. For more on the lUPAC, see the boxed essay What s In A Name Organic Nomenclature in Chapter 2. 

Alkanes are a class of saturated hydrocarbons with the general formula C H2n. -2- They contain no functional groups, are relatively inert, and can be either straight-chain (normal) or branched. Alkanes are named by a series of IUPAC rules of nomenclature. Compounds that have the same chemical formula but different structures are called isomers. More specifically, compounds such as butane and isobutane, which differ in their connections between atoms, are called constitutional isomers. 

In aromatic diazonium compounds containing an ionized hydroxyl group ( —O-) in the 2- or 4-position, it is necessary to consider delocalization of electrons and, therefore, two mesomeric structures (1.7a-1.7b) (see Sec. 4.2). This fact has implications for nomenclature compounds of this type are considered as quinone derivatives following IUPAC Rule C-815.3 (Exception) compounds of this class are called quinone diazides. As a specific compound 1.7a-1.7b is indexed in Chemical Abstracts as 4-diazo-2,5-cyclohexadien-l-one. If reference is made specifically to mesomeric structure 1.7b, however, it is called 4-diazoniophenolate. 

MDL Information Services, Inc. offers free software downloads at http // www.mdli.com/cgi/dynamic/downloadsect.html7uid= key= id = 1. These include AutoNom Standard (automatic nomenclature), which generates IUPAC chemical names directly from graphical structures created in ISIS/Draw or registered in ISIS/ Base. 

Divinyl sulfide, 25 630 Divinylsulfone method, for covalent ligand immobilization, 6 3961 Division of Chemical Nomenclature and Structure Representation (IUPAC),... 

We follow the 1979 IUPAC recommendations summarized in Polynuclear Aromatic Hydrocarbons Nomenclature Guide (Loening et al. 1990). The American Chemical Society also publishes the Ring Systems Handbook, which, ca. 1990, contained structural diagrams for over 70,000 unique ring systems (American Chemical Society, 1977 to present). 

For this review, heterophanes are considered to contain one or more heteroaromatic ring(s) bridged by a non-aromatic chain of atoms. Although a certain arbitrariness identifies (1) but not (2), as a heterophane, this definition focuses attention on the chemistry appropriate for this review and makes the volume of literature to be reviewed more manageable. Different nomenclature approaches for heterophanes have been proposed (70T5847,72T5183, 72TL2109) as alternatives for the currently accepted, complex IUPAC or Chemical Abstracts names, which actually obscure the phane structural element in these compounds. A proposal... 

The variety of methods of naming azo compounds which has been in use for many years may lead to considerable confusion, especially when attempts are made to name structural formulas of highly substituted dye molecules with several azo linkages. Furthermore, in regard to the older dye literature, an intuitive interpretation of an author s intention frequently seems more productive than a detailed analysis of the system of nomenclature which he may be using. An effort is made in this chapter to conform to either the IUPAC or the Chemical Abstracts system [la]. 

The nomenclature of boron hydride derivatives has been somewhat confusing and many inconsistencies exist in the literature. The structures of some reported boron hydride clusters are so complicated that only a structural drawing or graph, often accompanied by explanatory text, is used to describe them. Traditional nomenclature systems often can be used to describe compounds unambiguously, but the resulting descriptions may be so long and unwieldy that they are of litde use. The IUPAC (7) and the Chemical Abstract Service (8) have made recommendations, and nomenclature methods have now been developed that can adequately handle nearly all clusters compounds however, these methods have yet to be widely adopted. For the most part, nomenclature used in the original literature is retained herein. 

The systematic nomenclature for the cycloproparenes is confused because the fusion rule (IUPAC Rule A 21.3) requires that at least two rings of five or more members be present before the prefix cyclopropa may be used. Thus while l//-cyclopropa[a]- and -[/ naphthalene are correct for 10 and 11, respectively, 1 //-cyclopropabenzene is incorrect for 1. The Chemical Abstracts service and IUPAC are unanimous in naming 1 as bicyclo-[4.1. Ojhepta-1,3,5-triene la. Thus if the parent member is strictly named, not only does it differ from that of its higher homologues, but also it could be taken to imply a bond localized structure. Throughout this chapter parent 1 and its derivatives 5-9 are referred to as cyclopropabenzenes and numbered as shown for structure 1. 

As already pointed out, the nomenclature rules employed by Chemical Abstracts yield a unique index name for every structure, whereas the IUPAC Rules allow some latitude. This latitude is considerable with regard to the naming of substituted structures, and it is usually possible for an author to find in the rules a procedure suitable for any specific purpose. 

In most existing inventories, chemical identities are standardized through the use of CAS numbers, molecular formulas (chemicals with discrete structures), and IUPAC (International Union of Pure and Applied Chemistry) systematic nomenclature. Chemicals of unknown or variable composition, complex reaction products, and biological materials (UVCB), are usually listed alphabetically under subheadings or by definition.14 Some of the countries that have compiled various inventories include Australia, Canada, EU, Japan, Philippines, South Korea, and United States. 

So far, we have identified coordination compounds only by their chemical formulas, but names are also useful for many purposes. Some substances were named before their structures were known. Thus, K3[Fe(CN)g] was called potassium fer-ricyanide, and K4[Fe(CN)g] was potassium ferrocyanide [these are complexes of Fe (ferric) and Fe (ferrous) ions, respectively]. These older names are still used conversationally but systematic names are preferred to avoid ambiguity. The definitive source for the naming of inorganic compounds is Nomenclature of Inorganic Chemistry-IUPAC Recommendations 2005 (N. G. Connelly and T. Damhus, Sr., Eds. Royal Society of Chemistry, 2005). 

N.G. Connelly (Ed.) (2004). Nomenclature of Inorganic Chemistry. International Union of Pure and Applied Chemistry (lUPAC), Chemical Nomenclature and Structure Representation Division. Provisional Recommendations. http //www.iupac.org/reports/provisional/. 

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