Systematic names conversion

Polyhydroxyalkanoate synthase (systematic name acyl-CoA 3-hydroxybutyrate 0-acyltransferase EC 2.3.1. class) is responsible for the polymerizations of PHAs in vivo because it catalyzes the stereoselective conversion of (/ )-3-hydroxyacyl-CoA substrates to PHAs with the concomitant release of CoA (see Fig. 2) [3]. 

For instance, the systematic name of the compound 9-(2,6,6-trimethyl- 1 -cyclohexenyl)-3,7-dimethyl-2,4,6,8-nonatetraen-1 -ol would bog down a conversation hopelessly, although it is perfectly descriptive. This compound is usually called vitamin A. 

The answer to the second question—how to provide a name that is unique to a particular structure—is presented in the following section. It is worth noting, however, that being able to name compounds in a systematic way is a great help in deciding whether two structural formulas represent isomeric substances or are the same compound represented in two different ways. By following a precise set of rules, you will always get the same systematic name for a compound, regardless of how it is written. Conversely, two different compounds will always have different names. 

The systematic name of a compound is designed so that one may deduce from it the molecular structure of the compound, as indicated by its graphic formula. In other words, it is essentially a verbal substitute for the graphic formula and, in its most elaborate form, provides precisely the same structural information. However, it is a poor substitute most chemists if required to indicate the structure of a compound would draw the formula rather than write the name. Similarly, a systematic name is not often readily understood until it has been translated into its graphic equivalent. Inevitably, systematic names tend to be long, and ill-adapted for use in conversation they are useful only when to employ the graphic form would be impossible or inconvenient. 

Ideally, every organic substance should have a completely descriptive, systematic name to permit only one structural formula to be written for it. This ideal has been approached closely in some of the current nomenclature systems but, unfortunately, truly systematic nomenclature for very complicated compounds is often hopeless for conversational or routine scripto-rial purposes. As a result, we will at times resort to using (common) trivial names, especially if it is impractical to do otherwise. Clearly, the description 9-(2,6,6-trimethyl-l-cyclohexenyl)-3,7-dimethyl-2,4,6,8-nonatetraen-J-ol has phonetic disadvantages as a handy name for vitamin A ... 

The International Union of Biochemistry has recommended that enzymes have three names, namely a systematic name, which shows the reaction being catalysed and the type of reaction based on the classification in Table A7.1, a recommended trivial name and a four figure Enzyme Commission code (EC code). Nearly all systematic and trivial enzyme names have the suffix -ase. Systematic names show, often in semi-chemical equation form, the conversion the enzyme promotes and the class of the enzyme. Trivial names are usually based on the function of the enzyme but may also include or be based on the name of the substrate. However, some trivial names in current use are historical and bear no relationship to the action of the enzyme or its substrate, for example, pepsin and trypsin are the names commonly used for two enzymes that catalyse the breakdown of proteins during digestion. The Enzyme Commission s code is unique for each enzyme. It is based on the classification in Table A7.1 but further subdivides each class of enzyme according to how it functions. The full code is... 

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. 

Our intention in this chapter is to examine the challenges of extracting identihers from chemistry-related documents and the conversion of those identihers into chemical structures. The authors of this work each have well over a decade of experience in chemical structure representation and systematic nomenclature. We have been deeply involved in the development of software algorithms and software for the generation of systematic names and the conversion of chemical identihers into chemical structures.9 Although we have our own biases concerning approaches to the problem of N2S conversion, we have done our utmost to be objective in our review of the subject and comparison of approaches and performance. 

OpenEye s Lexichem,23 and ChemAxon52 has announced the imminent release of their own product early in 2008. As mentioned earlier, an Open Source Java library for the interpretation of IUPAC systematic names,34 OPSIN, has also been made available. In this chapter, most examples are based on Name=Struct and ACD/Name to Structure. We judge these programs to currently be the most advanced products in this area, but all considerations are general in nature and relevant to all of the conversion routines presently existing or still under development. 

For the conversion of systematic names, a more powerful and flexible approach must be based on the parsing of the chemical names and the application of syntax analysis. Figure 3.4 illustrates the principle steps of this procedure. The first step in the process, lexical analysis, splits the whole chemical name into a series of name fragments, known as lexemes, that have structural or grammatical meaning. Also... 

FIGURE 3.4 General steps of conversion of an unambiguous systematic name. 

The conversion of systematic names to their chemical structures is a time-consuming, skill-intensive process, and is not a minor undertaking. Such a project is guaranteed to take many years of development to cover the most important nomenclature operations. 

One of the primary issues with systematic nomenclature is that some names can appear systematic in nature but, in fact, are not. They can have the expected structure of a chemical name generated according to a rules-based system but are false systematic names, at least in their specific context. When the N2S conversion algorithms... 

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). 

These rules will allow you to name thousands of alkanes, and eventually you will learn the additional mles necessary to name many other kinds of compounds. The rules are important if you want to look up a compound in the scientific literature, because it usually will be listed by its systematic name. Nevertheless, you must still learn common names because they have been in existence for so long and are so entrenched in chemists vocabulary that they are widely used in scientific conversation and are often found in the literature. 

EC 4 Lyases catalyze cleavage and elimination reactions The enzymes cleave C— C, C—0, C—N and other bonds by elimination, leaving double bonds, or conversely adding groups to double bonds. The systematic name is formed according to the pattern, substrate group-lyase (the hyphen is an important part of the name and should not be omitted). Some names such as decarboxylase (elimination of CO2), dehydratase (elimination of water) are used. In some cases, the reverse reaction is more important, or the only one demonstrated, synthase (not synthetase) might be used. 

Some ionic compounds—such as NaCl (table salt) and NaHCOs (baking soda)— have common names, which are nicknames of sorts learned by familiarity. However, chemists have developed systematic names for different types of compounds including ionic ones. Even if you are not familiar with a compound, you can determine its systematic name from its chemical formula. Conversely, you can deduce the formula of a compound from its systematic name. 

The CAS Registry System contains not only the Registry File for structural data, but also the Nomenclature File, containing CA index names and synonyms, which may be other systematic names, common names, trade names, etc. (see Nomenclature Searching and Nomenclature Automatic Generation and Conversion) Currency, there are over 24 million chemical names in the Registry System. 

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