Unique names

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. 

How can we name alkanes so that each one has a unique name s... 

In Problem 2 5 you were asked to write structural formulas for the five isomeric alkanes of molecular formula C6H14 In the next section you will see how the lUPAC rules generate a unique name for each isomer... 

Selection of a name for a specific compound is heavily influenced by the purpose at hand communication to a general audience, communication with specialists, or storage/retrieval through archival indexes. The first requires the simplest rules possible the second requires the shortest names possible and the third requires rigid adherence to a set of rules that will reliably generate a unique name. The name chosen may be different for each situation, although that is not necessarily so. 

A data collection task updates the run database by associating a run number with the entry for the task and by setting the completion status in the entry. The run number is also used to assign a name to the data file created by the data collection task, thus guaranteeing that each data file has unique name. 

Merge the two lists of operations. If each action has a unique name, that s easy. For any operation that has specifications from both types, follow these steps. 

In the sc-PDB, a target is defined either as an enzyme from the PDB with a unique EC number, or a non-enzymatic protein with a unique name... 

To allow construction of a unique name, a single preferred constitutional repeating unit must be selected. 

In many cases, it will be noted that more than one name is suggested for a particular compound. Often a preferred name will be designated, but as there are several systematic or semi-systematic nomenclature systems it may not be possible, or even advisable, to recommend a unique name. In addition, many non-systematic (trivial) names are still in general use. Although it is hoped that these will gradually disappear from the literature, many are still retained for present use, although often in restricted circumstances. These restrictions are described in the text. The user of nomenclature should adopt the name most suitable for the purpose in hand. 

To obtain a unique name, a single preferred CRU must be selected. Therefore, rules have been developed that specify both seniority among subunits, that is, the point at which to begin writing the CRU, and also the direction in which to move along the chain to reach the end of the CRU. 

As for a single-strand polymer, a single preferred CRU must be selected in order to obtain a unique name. The CRU is usually a tetravalent group denoting attachment to four atoms and is named according to the usual rules of organic nomenclature. The name of the polymer is in the form poly(CRU). 

In February 1935, a fiber known in the laboratory as fiber 66 was produced that held promise for commercialization. The 66 refers to the number of carbon atoms in the reactants used to produce it. In the case of fiber 66, the two sixes refer to the six carbon atoms in adipic acid and six carbon atom in hexamethylenediamine, H2N(CH2)6NHr Fiber 66 was the first nylon produced. Like rayon, nylon is a generic term used for a group of synthetically produced polyamides. The name nylon was not introduced until 1938 after an extensive discussion by DuPont on what to call fiber 66. There are several versions of how the name nylon was coined, but one claims that nylon was a modification of norun (no run), which was modified into a unique name that could be used to market the product. DuPont officials had hoped to keep the name secret until the 1939 World s Fair, but leaks and patent preparation forced them to reveal the name early. DuPont did not trademark the name, but promoted the material genetically as nylon. 

Simple binary and ternary compounds can be named by using a few simple rules, but systematic rules are required to name the millions of organic compounds that exist. Rules for naming compounds have been established by the International Union of Pure and Applied Chemistry (IUPAC). The IUPAC name stands for a compound that identifies its atoms, functional groups, and basic structure. Because of the complexity of organic compounds, thousands of rules are needed to name the millions of compounds that exist and the hundreds that are produced daily. The original intent of the IUPAC rules was to establish a unique name for each compound, but because of their use in different contexts and different practices between disciplines, more than one name may describe a compound. IUPAC rules result in preferred IUPAC names, but general IUPAC names are also accepted. 

SAMPLE SOLUTION (a) Like the dihydroxybenzenes, the isomeric trihydroxy-benzenes have unique names. Pyrogallol, used as a developer of photographic film, is 1,2,3-benzenetriol. The three hydroxyl groups occupy adjacent positions on a benzene ring. 

The most recent recommendations by IUPAC for naming heterocyclic skeletons include only a small number of basic nomenclature systems, and, as a consequence of its need to provide unique names, the number of systems employed by Chemical Abstracts is even smaller. Of the systems now to be outlined, most are described in detail in the Appendix (to which reference is made where appropriate) the following text will cover only the general principles involved. Many of the systems are modifications of those used for carbocycles. 

As will be apparent, the foregoing descriptions of the systems available give only a broad outline of the operations involved. For each system, derivation of a unique name and numbering for a particular skeleton requires use of the full text of the appropriate rules provided in the Appendix. Construction of the name is governed by lists of priorities, the application of which is illustrated in many of the examples. However some general aspects of the use of the systems will be considered here, in particular their applicability in various contexts, and a number of specific problems. 

Alternative rules within the latter system may allow assigning more than one unambiguous name to a compound. The controlled alphabetic listing in the Chemical Substances Index of Chemical Abstracts Service (CAS), a part of the ACS, requires that each compound have a unique name. This convention ensures that all information for a single compound such as H2n—CH2—CH2—OH. which can be unambiguously named 2-aminoethanol. 2-aminoethyl alcohol, 2-hydroxyethylamine, etc., will appear in the index under one name ethanol, 2-amino-. Because universal... 

Fig. 11.7. Random section of the COSMO frag database file five-digit atom word are separated by blanks. The first 8 words are the atom similarity codes of order 0 to 7, followed by 2 by-codes containing additional information. At the end of each line the molecule of each atom is marked, using a nine-letter unique name constructed from the molecule identity index, followed by information on the neighbor atoms and implicit hydrogens. In this section all atoms are identical up to the second order, while atoms 5 and 6 are the most identical (up to fifth order).

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