Nomenclature, systematic

In chemistry, chemical structures have to be represented in machine-readable form by scientific, artificial languages (see Figure 2-2). Four basic approaches are introduced in the following sections trivial nomenclature systematic nomenclature chemical notation and mathematical notation of chemical structures. 

Wheeler, T.A. and Chisholm, L.A. (1 995) Monogenea versus Monogenoidea the case for stability in nomenclature. Systematic Parasitology 30, 159-164. 

As was done in CHEC-I <84CHEC-1(1)630>, the nomenclature in this chapter follows the borane and the borate nomenclature. Systematic rules are avoided if trivial names are available. If this is not the case, the general nomenclature of heterocycles is used. The following description of the different types of compounds elucidates structures and nomenclature (l)-(22). 

Nomenclaturists use the terms trivial and systematic to describe two major divisions of nomenclature. Systematic nomenclature is based on established principles so that it can be extended in a logical way to describe known, new, and hypothetical compounds. A trivial nomenclature is one established by rule of thumb and includes many of the older names (spirit of salt, aqua regia, etc.) and lab nomenclatures (the green chelate, etc.). 

Queiroz, K. (2006). The PhyloCode and the distinction between taxonomy and nomenclature. Systematic Biology, 55 160-2. 

Enzyme commission of the International Union of Biochemistry and Molecular Biology (lUBMB) established two enzyme nomenclatures systematic and trivial. According the systematic nomenclature all enzymes are divided upon 6 classes l.Oxidoreductases 2. Transferases 3. Hydrolyses 4. Lyases cleaving C-C C-O, C-N bonds 5. Isomerases, and 6. indication ofbond formed. 

For simple compounds the main reference uses the systematic I.U.P.A.C. nomenclature, but other nomenclature is cross-referenced to the systematic name. 

Enzymes are classified in terms of the reactions which they catalyse and were formerly named by adding the suffix ase to the substrate or to the process of the reaction. In order to clarify the confusing nomenclature a system has been developed by the International Union of Biochemistry and the International Union of Pure and Applied Chemistry (see Enzyme Nomenclature , Elsevier, 1973). The enzymes are classified into divisions based on the type of reaction catalysed and the particular substrate. The suffix ase is retained and recommended trivial names and systematic names for classification are usually given when quoting a particular enzyme. Any one particular enzyme has a specific code number based upon the new classification. 

Nomenclature is the compilation of descriptions of things and technical terms in a special field of knowledge, the vocabulary ofa technical language. In the history of chemistry, a systematic nomenclature became significant only rather late. In the early times of alchemy, the properties of the substance or its appearance played a major role in giving a compound a name. Libavius was the first person who tried to fix some kind of nomenclature in Alckeinia in 1,597. In essence, he gave names to chemical equipment and processes (methods, names that are often still valid in our times. 

The systematic lUPAC nomenclature of compounds tries to characterize compounds by a unique name. The names are quite often not as compact as the trivial names, which are short and simple to memorize. In fact, the lUPAC name can be quite long and cumbersome. This is one reason why trivial names are still heavily used today. The basic aim of the lUPAC nomenclature is to describe particular parts of the structure (fi agments) in a systematic manner, with special expressions from a vocabulary of terms. Therefore, the systematic nomenclature can be, and is, used in database systems such as the Chemical Abstracts Service (see Section 5.4) as index for chemical structures. However, this notation does not directly allow the extraction of additional information about the molecule, such as bond orders or molecular weight. 

Neither a trivial name nor the systematic nomenclature, which both represent the structure as an alphanumerical (text) string, is ideal for computer proccs.sing. The reason is that various valid compound names can describe one chemical structure (Figure 2-6). As a consequence, the name/structure correlation is unambiguous but not unique. Nowadays, programs can translate names to structures, and. structitrcs to names, to make published structures accessible in electronic journals (see also Chapter (I, Section 2 in the Handbook). 

UJPAC nomenclature standardized systematic classification include stcrcochcmistr) widespread unambiguous allow reconstruction extensive nomenclarurc rules altcrnalivc names are allow-ed complicated names... 

While the trivial and trade nomenclature in most cases has accidental character, the lUPAC Commission has worked out a series of rules [4] which allow the great majority of structures to be represented uniformly, though there still exists some ambiguity within this nomenclature. Thus, many structures can have more than one name. It is important that the rules of some dialects of the lUPAC systematic nomenclature are transformed into a program code. Thus, programs for generating the names from chemical structures, and vice versa (structures from names) have been created [5] (see Chapter II, Section 2 in the Handbook). 

A more detailed account of the history of organic nomenclature may be found in the article The Centen nial of Systematic Organic Nomenclature in the No vember 1992 issue of the Journal of Chemical Educa ton (pp 863-865)... 

The generic name of a drug is not directly de rived from systematic nomenclature Furthermore different pharmaceutical companies will call the same drug by their own trade name which is differ ent from its generic name Generic names are in vented on request (for a fee) by the U S Adopted Names Council a private organization founded by the American Medical Association the American Pharmaceutical Association and the U S Pharma copeial Convention... 

The names cited are common names which have been m widespread use for a long time and are acceptable m lUPAC nomenclature We will introduce the systematic nomen clature of these ring systems as needed m later chapters... 

Sulfides are sometimes infor mally referred to as thioethers but this term is not part of systematic lUPAC nomenclature... 

It IS hard to find a class of compounds in which the common names of its members have influenced organic nomenclature more than carboxylic acids Not only are the common names of carboxylic acids themselves abundant and widely used but the names of many other compounds are derived from them Benzene took its name from benzoic acid and propane from propionic acid not the other way around The name butane comes from butyric acid present m rancid butter The common names of most aldehydes are derived from the common names of carboxylic acids—valeraldehyde from valeric acid for exam pie Many carboxylic acids are better known by common names than by their systematic ones and the framers of the lUPAC rules have taken a liberal view toward accepting these common names as permissible alternatives to the systematic ones Table 19 1 lists both common and systematic names for a number of important carboxylic acids... 

Systematic nomenclature (Section 2 11) Names for chemical compounds that are developed on the basis of a prescnbed set of rules Usually the lUPAC system is meant when the term systematic nomenclature is used... 

Systematic names formed by applying the principles of substitutive nomenclature are single words except for compounds named as acids. First one selects the parent compound, and thus the suffix, from the characteristic group listed earliest in Table 1.7. All remaining functional groups are handled as prefixes that precede, in alphabetical order, the parent name. Two examples may be helpful ... 

Systematic nomenclature Systemic antimycotics Systhane Syzygiol Szaibelyite... 

A systematic nomenclature for nAChRs has yet to evolve. An N nomenclature describes receptors present ia muscle as N. These are activated by phenyltrimethylammonium (PTMA) (15) and blocked by t5 -tubocurariae (16) and a-bungarotoxiu (a-BgT) (17). N2 receptors are present ia ganglia and are activated by l,l-dimethyl-4-phenylpipera2inium (DMPP) (18) and blocked by trimethaphan (19) and bis-quatemary agents, with hexamethonium (20) being the most potent. 

The practice of assigning ad hoc names to organic compounds was neither avoidable, nor burdensome when only a small number of compounds were recognized. Such ad hoc names are termed "trivial" or "traditional," to indicate that they contain no encoded stmctural information. They are useful for common compounds, and many of them are retained to this day, but they are not helpful in understanding chemical relationships. As they proliferated, the number and variety of them became unmanageable. The development of systematic nomenclature was driven by this circumstance, and was made possible by advances in understanding and determining the stmcture of molecules. 

This was a great advance, as complex hydrocarbons of various kinds could be clearly named if their stmctures were known. The Geneva system, modified and expanded by subsequent Commissions, is used systematically in the fourth and fifth editions of Be /stem s Handbuch der Organischen Chemie (1), and as the basis of lUPAC nomenclature. In 1992 a commemorative symposium on the centennial anniversary of the Geneva Conference was held in Geneva (45). 

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