IUPAC nomenclature , literature

The literature gives a wide range of practical guidelines for the evaluation of method performance characteristics [58]. Besides the diversity of approaches, also the terminology and way of reporting results vary widely. Differences may occur depending on the purpose and the application field of the method, and validation studies may become more difficult as the complexity of the analysis increases [86]. In what follows, terms and formulas are taken from the accepted IUPAC nomenclature for the presentation of results of chemical analysis [66]. For each validation parameter, definitions, ways of expression, determination guidehnes, and acceptance criteria are reported in Table 5. 

Another name for the benzyloxycarbonyl group is carbobenzoxy. This name, and its abbreviation Cbz, are often found in the older literature, but are no longer a part of IUPAC nomenclature. 

Since the new IUPAC recommendations [5], the nomenclature of quinic acid isomers is very confusing in the literature. Therefore, the latest IUPAC nomenclature is used throughout this paper instead of the older, but still useful, nomenclature. In the IUPAC nomenclature quinic acid is now treated as cyclitol. In the preferred configuration, the carboxy group and the C-4 and C-5 hydroxy groups are equatorial, with the C-l and C-3 hydroxy groups are axial. In the IUPAC system, the former 3-O-acylquinic acids are now renamed 5-O-compounds, and the... 

The resonance structures of the 2-substituted pyrazole 1-oxides 74 are discussed in Section 1.1.1. According to IUPAC nomenclature, structure 86 is a 1-substituted lH-pyrazole 2-oxide since the rules dictate that when R=H the indicated hydrogen position takes numbering precedence. Other names found in the literature are 1-substituted pyrazole 2-oxides or 1-substituted 2-oxo-1 H-pyrazoles. Frequently the numbering is switched to give the names 2-substituted 2H-pyrazole 1-oxide, 2-substituted pyrazole... 

The resonance structures of the 3-substituted 1,2,3-triazole 1-oxides 456 are discussed in Section 1.1.1. 3-Substituted 1,2,3-triazole 1-oxides 456 are strictly according to IUPAC nomenclature 1-substituted 1H-1,2,3-triazole 3-oxides since when R=H the hydrogen position takes numbering precedence. The alternative, correct name 1-subshtuted 3-oxo-lH-l,2,3-tri-azoles has not been adopted in the literature. In the present review the most commonly used naming is adopted calling structure 456 a 3-sub-stituted 1,2,3-triazole 1-oxide. This naming is accepted by IUPAC, Chem. Abstr. Autonom. 

Figure 5.5.12-1 Alternate nomenclatures for the retinoids associated with vision. A the Karrer based nomenclature adopted by the IUPAC. B the systematic nomenclature proposed by Frickel and others. C a second systematic nomenclature found in the literature. D the modified pictograph of the IUPAC nomenclature used in this work.

Since many triazolopyridines were prepared as nucleoside mimics, they are often described in the literature using the nucleoside nomenclature format in lieu of the systematic IUPAC nomenclature. Some examples (l)-(3) are shown below in Table 1. 

Nomenclature The most recent IUPAC nomenclature is stressed throughout the book, but common nomenclature is also discussed and used to develop students familiarity. Teaching only the IUPAC nomenclature might be justifiable in theory, but such an approach would handicap students in their further study and use of the literature. Much of the literature of chemistry, biology, and medicine uses common names such as methyl ethyl ketone, isovaleric acid, methyl tert-butyl ether, -y-aminobutyric acid, and e-caprolactam. This book emphasizes why systematic nomenclature is often preferred, yet it encourages familiarity with common names as well. 

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. 

Since the early 1970s a panel convened by the International Union of Pure and Applied Chemistry and the International Union of Biochemistry and Molecular Biology has been working to formulate recommendations for carbohydrate nomenclature that meet developing needs of research and electronic data handling, while retaining links to the established literature base on carbohydrates. The realization of these endeavors is presented here in the final document Nomenclature of Carbohydrates, which provides a definitive reference for current researchers, both in the text version and in the version accessible on the World Wide Web (http //www.chem.qmw.ac.uk/iupac/2carb/), where amendments and revisions are maintained. 

According to the IUPAC-IUB Enzyme Nomenclature,11 pectinesterase belongs to the carboxyl ester hydrolases (EC 3.1.1.11) and has the systematic name pectin pectyl-hydrolase. The literature also contains the expressions pectin methylesterase, pectin demethoxylase, and pectin methoxylase for the same enzyme. The old name pectase,... 

In addition, other systems of nomenclature for AHLs have also appeared in the literature describing them as derivatives of furanone, y-butyrolactone or 4-butanolide. For example, the above V.fischeri autoinducer can also be named as (S)-N-(3-oxohexanoyl)-3-aminodihydro-2(3H)-furanone,(S)-a-(3-oxohexa-noyl)amino-y-butyrolactone or (S)-2-(3-oxohexanoyl)amino-4-butanolide (another IUPAC name) [27]. 

The nomenclature for this homologous series is somewhat confused. The term PANs has been used historically to denote peroxyacyl nitrates, and this terminology continues to be used extensively in the literature, despite the lack of adherence to traditional IUPAC rules of nomenclature. Because the PANs can be considered to be mixed anhydrides of carboxylic acids and nitric acid, another suggestion (Roberts, 1990) has been peroxyacetic nitric anhydride for CH,C(0)00NO2 and peroxy carboxylic nitric anhydrides for the whole class of compounds. Although it does not follow the IUPAC rules, it would be consistent with the widespread use of the name PAN but also reflect the structure more accurately. Table 6.20 shows the structures and commonly used names of some PANs that have been observed in the atmosphere and/or in laboratory studies. 

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 general formula for boric acid esters is B(OR)3. The lower molecular weight esters such as methyl, ethyl, and phenyl are most commonly referred to as methyl borate [121 -43-7], ethyl borate [150-46-9], and phenyl borate [1095-03-0], respectively. Some of the most common boric acid esters used in industrial applications are Us ted in Table 1. The nomenclature in the boric acid ester series can be confusing. The IUPAC committee on boron chemistry has suggested using thalkoxy- and triaryloxyboranes (5) for compounds usually referred to as boric acid esters, trialkyl (or aryl) borates, trialkyl (or aryl) orthoborates, alkyl (or aryl) borates, alkyl (or aryl) orthoborates, and in the older literature as boron alkoxides and aryloxides. Cyclic boric acid esters, which are trimeric derivatives of metaboric acid (HB02), are known as boroxines (1). 

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. 

Garboranes. The term carborane is widely used in American literature as a contraction of the IUPAC approved nomenclature carbaborane. The first carboranes, isomers of C2B3H5, C2B4H6, and C2B5H7, were prepared in the mid-1950s at Olin Mathiesen. These carboranes were obtained as a mixture in low yield from the reaction of pentaborane(9) with acetylene in a silent electric discharge. The discovery of the icosahedral... 

Two types of fusion nomenclature are available of these the older Stelzner system" is not recommended for use by IUPAC (except as in Rule B-23.5) or by Chemical Abstracts. Nevertheless, it will be described briefly here since it still appears commonly in the literature. The principles of both systems are best understood in application to polycar bocycles. 

The prefix selenopheno is used to denote selenophene fusion in this chapter, following the greater part of the literature in the field. Chemical Abstracts and the IUPAC Rules of Nomenclature prefer the (possibly confusing) form selenolo. [Editors.]... 

The scope of this problem can be indicated by a brief consideration of the stereochemical nomenclature of hydroxy derivatives of the bicyclic terpenes. For the parent bicyclic hydrocarbon compound known in the literature at present as cam-phane, the name "bomane is recommended in this report. (Reasons for choosing "bornane are discussed later under "The Bornane Hydrocarbons .) A mono-hydroxy derivative of bornane, on the basis of IUPAC rules (41), would be named as a bornanol. Two such derivatives have the common terpene names, bomeol and isobomeol these names, on the basis of recommendations in this report would both become 2-bornanol. Obviously, this is inadequate and additional designations are necessary to distinguish between die two stereoisomers. 

In replacement nomenclature, the name of a heterocyclic compound is formed by prefixing a terms, such as oxa , thia , aza , etc. to the name of the corresponding cyclic hydrocarbon. As IUPAC Rule B-4 states that the replacement method should be applied to a homocyclic hydrocarbon, we use pentalene for this purpose. The replacement procedure forbids the use of heterocyclic parent structures and for this reason the name thiathiophthene , which is found in the literature, is not in compliance with IUPAC recommendations. Another name which is sometimes found is thiothiophthene , which is even worse because of an incorrect use of the prefix thio . 

---