Ambiguous systematic names

FIGURE 3.7 Chemical structure and IUPAC name of Simvastatin. 

Chemical Information Mining Facilitating Literature-Based Discovery 

FIGURE 3.8 Potential ambiguity of names with missing locants or parentheses. 

A similar exampleis 4-methylthiophenol. This name also allows thegeneration of two structures, but here the situation is reversed and most cases refer to 4-methyl(thiophenol) (or 4-methylbenzenethiol according to current naming conventions). 

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These contracted names of heterocyclic nitrogen compounds are retained as alternatives for systematic names, sometimes with indicated hydrogen. In addition, names of 0x0 derivatives of fully saturated nitrogen heterocycles that systematically end in -idinone are often contracted to end in -idone when no ambiguity might result. For example. 

If derivatives are to be named on the basis of the trivial name, the component cited last in the systematic name receives locants with no primes, the preceding component singly-primed locants, etc. However, naming of trisaccharide and higher oligosaccharide derivatives systematically is preferred, to avoid ambiguity. 

Like poly(ethylene), there are formal problems with the nomenclature of this polymer, since its lUPAC name, poly(propene), is also rarely if ever used hy polymer chemists. Since, in practice, no ambiguity is associated with the non-systematic name, this is the one that is generally used, as it will he throughout this hook. 

Each enzyme is assigned two names. The first is its short, recommended name, convenient for everyday use. The second is the more complete systematic name, which is used when an enzyme must be identified without ambiguity. 

The systematic or IUPAC name is 2-methylbuta-l,3-diene. This means that the longest chain of carbon atoms is 4 (like butane), giving the buta part of the name it is an alkene ( ene represents an alkene) with two ( di ) double bonds starting on carbon atoms 1 and 3, giving the name buta-1, 3-diene, and the methyl group is attached to the carbon atom 2 ( 2-methyl ). (When no ambiguity can arise, the name may also be written 2-methyl-l, 3-butadiene.) From this point forward these more systematic names will be used. 

In this case there is only a single methyl group at each locations and so there is no ambiguity however, there will be more problems with increasing branching, especially when rings are introduced. Meanwhile, upon comparing the above nodal name and the proposed systematic name,... 

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). 

To avoid ambiguity, the name should not be used as the root for the systematic nomenclature of carboca-tions. The corresponding difficulty confused carbonium ion nomenclature for many years. For example, the term ethylcarbonium ion has at times been used to refer either to CH3CH2+ (ethyl cation) or (correctly) to CH3CH2CH2+ (propyl cation). 

The ketoses are classified as 2-ketoses, 3-ketoses, etc., following the carbonyl position on the chain. The 2 of 2-ketoses, a common natural structure, can be removed. The suffix ose is replaced by ulose in the parent name. Likewise, fructose is a 2-hexulose, or more simply, a hexulose. For the complete name, it is preceded by the configuration descriptor. The systematic name of fructose 4.37 would be D-araZ>Z o-2-hexulose. In the case of 2-ketoses, there is no possible ambiguity for the configuration of pyranoses and furanoses. The nomenclature is copied from that of aldoses as, for example, /3-D-fructopyranose 4.38. Methyl glycoside 4.39 of sialic acid is called methyl 5-acetamido-3,5-dideoxy-D-gZycera-a -D-gaZacfo-2-nonulopyranosidonic acid. 

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. 

Cross-references are inserted in the index for many common names and for some systematic names. Trademark names appear in the index. Names that are incorrect, misleading, or ambiguous are avoided. Formulas are given very frequendy in the text to help in identifying compounds. The spelling and form used, even for industrial names, follow American chemical usage, but not always the usage of Chemical Abstracts (eg, coniine is used instead of (S)-2-propylpiperidine, aniline instead of benzenamine, and acrylic acid instead of 2-propenoic acid). 

Systematic names are easier and less ambiguous than common names. Whenever possible, we will use this system of nomenclature. The older, common names (-ous, -ic) are less specific furthermore, they often use the Latin names of the elements (for example, iron compounds use/err-, from ferrum, the Latin word for iron). 

It should be pointed out that currently both trivial and systematic names are commonly used for naming the heterocyclic compounds. For example, an organic chemist will recognize without any difficulty the structures connected to names such as furane, pyrrole, pyrrolidine, pyrazole, imidazole, pyridine, or piperidine, despite the fact that all these names are trivial. On the other hand, the complex heterocycles require more sophisticated approaches in order to avoid ambiguity and correctly translate the chemical strucmre into the name. For these, compound names are often made using either trivial name (e.g., indazole for benzopyrazole, benzimidazole, indole, and isoindole) or the Hantzsch-Widman nomenclature, for example, 1,2,3- or 1,2,5-oxadiazoles, 1,3-dioxolane, 1,2- or 1,3-dithiolane, and 1,3- or 1,4-dioxane. It should be noted that the Hantzsch-Widman nomenclature treats the unsaturated heterocycle with maximum number of conjugated double bonds as parent compound. This adds another layer of complexity, giving rise to names such as... 

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). 

Since this notation is not systematic, some ambiguities can occur for instance, H2TMeP is for some authors (and in this chapter) tetra-meso-methylporphyrin but for some others it is 2,3,10,12-tetramethylporphyrin. For the last-mentioned compound, we use its full name. 

SAMPLE SOLUTION (a) The molecule has a tert-butyl group bonded to a nine-membered cycloalkane. It is tert-butylcyclononane. Alternatively, the tert-butyl group could be named systematically as a 1,1-dimethylethyl group, and the compound would then be named (1,1-dimethylethyl)cyclononane. (Parentheses are used when necessary to avoid ambiguity. In this case the parentheses alert the reader that the locants 1,1 refer to substituents on the alkyl group and not to ring positions.) ... 

Secondary and tertiary amines, which have two and three substituents on nitrogen, commonly are named as N-substituted amines. As for substituted amides, N is included to indicate that the substituent is on the nitrogen atom unless there is no ambiguity as to where the substituent is located. Systematic nomenclature of secondary and tertiary amines is related to the systematic ether nomenclature discussed in Section 7-3 ... 

This example demonstrates that one of the main challenges for an N2S conversion algorithm applied to data mining is the conversion of chemical names that are not strictly systematic, are ambiguous, or include typographical errors or misprints. 

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