Naming chemical compounds

Chapter 2 provides an index of synonyms for chemical compound names. Data sections of the handbook that provide chemical specific information on fire and explosion, and chemical reactivity identify the chemical compound by its most common chemical name. Therefore, if a synonym name is known, the reader may refer to Chapter 2 for a listing of synonyms that cross reference the name to the most common chemical compound name. 

Following is an index of synonyms corresponding to common chemical compound names. Sections of file handbook that provide information on the hazardous properties of chemicals, reference the chemical by its most common chemical compound name. This index should be used to identify a common name if the synonym is known. 

The use of proper chemical nomenclature is essential for effective scientific communication. More than one million new substances are reported each year, each of which must be identified clearly, unambiguously, and completely in the primary literature. Chemical compounds are named according to the rules established by the International Union of Pure and Applied Chemistry (IUPAC), the International Union of Biochemistry and Molecular Biology (IUBMB) [formerly the International Union of Biochemistry (IUB)], the Chemical Abstracts Service (CAS), the Committee on Nomenclature, Terminology, and Symbols of the American Chemical Society, and other authorities as appropriate. For more information on naming chemical compounds, refer to the bibliography in Chapter 18. This chapter gives the editorial conventions and style points for chemical compound names. 

Textual names have the advantage of being machine-readable, but many chemical compound names are derived in the absence of structural information. Common or trivial names were frequently given to compounds based on their properties or methods of extraction (because their structural information was originally an unknown). For example, mandelic acid was extracted from bitter almonds, and its name is derived from Mandel, the German word for almond (Merck 1989). 

In 1971, Kuhnert-Brandstatter applied thermomicroscopy to an even narrower segment of chemical compounds, namely, organic compounds of medicinal benefit (20). Her research efforts characterized many polymorphic systems in the pharmaceutical industry. Tynan and Von Gutfeld developed a vacuum sample holder for use on an optical microscope. This accessory had the ability to characterize small samples in the 30 to 800 K temperature range (21). Schultze presented a design for a high-temperature microscope-differential thermal analyzer, which explored this role of the combination technique in the high-temperature research field (22). 

Entity extraction is the process of tagging things in the text as specific items such as genes, cell lines, people, chemical compounds, and so on. Two specific requirements for entity extraction are unique and critical to biomedical applications of text mining. Gene name disambiguation and chemical compound name tagging require different approaches. 

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. 

Much of this handbook is concerned with the how and why of crystallization and crystallizer design. This chapter will focus on the crystallization of one particular class of chemical compounds, namely the proteins. In the timeline of crystallization, protein crystallization is a newcomer. The first mention of protein crystal formation, roughly 150 years ago, involved crystallizing hemoglobin from the blood of various species (Lehman 1853 Reichert and Brown 1909 Debru 1983 McPherson 1991). This work was followed by the crystallization of a variety of proteins from plants to egg white (Sumner 1926). These early studies were pivotal in establishing that enzymes are proteins (Dounce and Allen 1988). The use of protein crystallization in purification and classification of biological chemicals resulted in the Nobel Prize for Chemistry being awarded to Sumner, Nothrop, and Stanley in 1946. 

For example, in a system containing calcium carbonate, calcium oxide, and carbon dioxide, there are three independent chemical compounds, namely CaCOs, CaO, and CO2. These are connected by a chemical reaction equation such as CaCOs — CaO -1- CO2. Consequently, the number of components is reduced by 1... 

In 1814, J.J. Berzelius succeeded for the first time in systematically naming chemical substances by building on the results of quantitative analyses and on the definition of the term "element by Lavoisier. In the 19th century, the number of known chemical compounds increased so rapidly that it became essential to classify them, to avoid a complete chaos of trivial names (see Section 2.2.4). 

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). 

Figure 2-6. Various logical compound names can describe one chemical structure.

Line notations represent the structure of chemical compounds as a linear sequence of letters and numbers. The lUPAC nomenclature represents such a kind of line notation. However, the lUPAC nomenclature [6] makes it difficult to obtain additional information on the structure of a compound directly from its name (see Section 2.2). 

The commercial 2D structure editor. Chemistry 4D-Draw, from Chemlnnovativc Software Inc., includes two additional special modules besides conventional chemical drawing tools. NamExpert provides the interpretation ofa compound name according to the lUPAC nomenclature to create the corresponding chemical structure. The latter can be represented in three different styles the shorthand. Kckulc. or semi-structural formula. In contrast to NamExpert, the Nomenclature module assigns lUPAC names to drawn structures. 

The CAS Registry contains information on all the chemical compounds published in the literature since 1957. The sources of these 21 million compounds are 9000 international journals containing chemical information. The database includes CAS Registry Numbers, the CAS name (not conforming to the lUPAC convention) with synonyms, and molecular and structural formulas. The CAS provides a weekly update (see Section 5.4). 

Next, the power and the benefits of reaction center or reaction sub.structurc searching (see Section 3.3) will be illustrated. Figure 10.3-26 shows some of the hits obtained in a search for reactions that form a C-C bond. Intentionally, only the names of the starting materials and products of these reactions are given in order to emphasize that the common feature of these reactions cannot be derived from coding chemical compounds by name. Only a search by reaction center can expose the similarity in these reactions. The next logical steps would then be to explore whether these reactions have more in common than just forming a C-C bond. 

The lUPAC rules are not the only nomenclature system in use today Chemical Abstracts Service sur veys all the worlds leading scientific journals that publish papers relating to chemistry and publishes brief abstracts of those papers The publication Chemical Abstracts and its indexes are absolutely es sential to the practice of chemistry For many years Chemical Abstracts nomenclature was very similar to lUPAC nomenclature but the tremendous explosion of chemical knowledge has required Chemical Abstracts to modify Its nomenclature so that its indexes are better adapted to computerized searching This means that whenever feasible a compound has a sin gle Chemical Abstracts name Unfortunately this Chemical Abstracts name may be different from any of the several lUPAC names In general it is easier to make the mental connection between a chemical structure and its lUPAC name than its Chemical Abstracts name... 

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... 

Two-Dimensional Representation of Chemical Structures. The lUPAC standardization of organic nomenclature allows automatic translation of a chemical s name into its chemical stmcture, or, conversely, the naming of a compound based on its stmcture. The chemical formula for a compound can be translated into its stmcture once a set of semantic rules for representation are estabUshed (26). The semantic rules and their appHcation have been described (27,28). The inverse problem, generating correct names from chemical stmctures, has been addressed (28) and explored for the specific case of naming condensed benzenoid hydrocarbons (29,30). 

Both common and systematic names of compounds are used throughout this volume, depending on which the Editor-in-Chief felt was more appropriate The Chemical Abstracts indexing name for each title compound, if it differs from the title name, is given as a subtitle Systematic Chemical Abstracts nomenclature, used in both the 9th and 10th Collective Indexes for the title compound and a selection of other compounds mentioned in the procedure, is provided in an appendix at the end of each preparation. Registry numbers, which are useful in computer searching and identification, are also provided in these appendixes. Whenever two names are concurrently in use and one name is the correct Chemical Abstracts name, that name is adopted. For example, both diethyl ether and ethyl ether are normally used. Since ethyl ether is the established Chemical Abstracts name for the 8lh Collective Index, it has been used in this volume The 9th Collective Index name is 1,1 -oxybisethane, which the Editors consider too cumbersome. 

Chemical or Chemical Category Name (Enter only one name exactly as it appears on tr>e 313 list. ] Lead Compounds... 

Chemical Designation - A list of common synonyms is given. Synonym names are alternative systematic chemical names and commonly used trivial names for chemicals. An index of synonyms is provided at the end of the handbook to assist the reader in identifying a particular chemical and researching chemical hazards information in the event that the common name of the chemical is not known. The data field also contains the chemical formula. The chemical formula is limited to a commonly used one-line formula. In the case of some organic chemical compounds it has not been possible to represent the chemical structure within such limitation. 

The three specific topics explicitly mentioned in the title of Pdlyh s paper, namely Groups, Graphs, and Chemical Compounds, each has a section to itself following the Introduction. A fourth section, equally important, deals with the determination of asymptotic results... 

In a complementary study of the interaction between polyanilinc and ITO, oligomeric polyaniline model compounds, namely phenyl-capped amino (PC2) and imino (PC20X) dimers [113, 114] have been used. The chemical structures of the polyaniline oligomers are displayed in Figure 5-20. Both substances are soluble in... 

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