Structure representation nomenclature

A nomenclature or notation is called unambiguous if it produces only one structure. However, the structure could be expressed in this nomenclature or notation by more than one representation, all producing the same structure. Moreover, uniqueness" demands that the transformation results in only one - unique -structure or nomenclature, respectively, in both directions. 

Divinyl sulfide, 25 630 Divinylsulfone method, for covalent ligand immobilization, 6 3961 Division of Chemical Nomenclature and Structure Representation (IUPAC),... 

The aim of this chapter is to introduce and summarize the work on polymer nomenclature which has emanated, firstly, from the Commission on Macromolecular Nomenclature of the lUPAC Macromolecular Division and, latterly, from the Sub-Committee on Polymer Terminology of the lUPAC Macromolecular (now Polymer) Division, jointly with the lUPAC Chemical Nomenclature and Structure Representation Division. The Commission on Macromolecular Nomenclature is henceforth denoted as the Commission . 

The names of inorganic and coordination polymers are based on the same fundamental principles that were developed for organic polymers. As in the nomenclature of organic polymers, these rules apply to structural representations that may at times be idealised and do not take into account irregularities, chain imperfections or random branching. 

With the variety of chemical substance representations, i.e., fragment codes, systematic nomenclature, linear notations, and connection tables, a diversity of approaches and techniques are used for substructure searching. Whereas unique, unambiguous representations are essential for some registration processes, it is important to note that this often cannot be used to advantage in substructure searching. With connection tables, there is no assurance that the atoms cited in the substructure will be cited in the same order as the corresponding atoms in the structure. With nomenclature or notation representation systems, a substructural unit may be described by different terms or... 

The conversion from a connection table to other unambiguous representations is substantially more difficult. The connection table is the least structured representation and incorporates no concepts of chemical significance beyond the list of atoms, bonds, and connections. A complex set of rules must be applied in order to derive nomenclature and linear notation representations. To translate from these more structured representations to a connection table requires primarily the interpretation of symbols and syntax. The opposite conversion, from the connection table to linear notation, nomenclature, or coordinate representation first requires the detailed analysis of the connection table to identify appropriate substructural units. The complex ordering rules of the nomenclature or notation system or the esthetic rules for graphic display are then applied to derive the desired representation. 

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. 

Wisniewski, J.L. (2003) Chemical nomenclature and structure representation algorithmic generation and conversion, in Handbook of Chemoinformatics, Vol. 1 (ed. J. Gasteiger), Wiley-VCH Verlag GmbH, Weinheim, Germany, pp. 51-79. 

N.G. Connelly (Ed.) (2004). Nomenclature of Inorganic Chemistry. International Union of Pure and Applied Chemistry (lUPAC), Chemical Nomenclature and Structure Representation Division. Provisional Recommendations. http //www.iupac.org/reports/provisional/. 

In the previous three chapters we have progressed from atoms and electrons to bonds and molecules to sophisticated structural representations and nomenclature of organic molecules. Chapter 4 uses this knowledge of organic structure to introduce organic chemical reactions. 

The relative ranking of ligands for the description of the stereochemical properties of a molecule is the most utilized and accepted principle throughout stereochemical nomenclature. This is not yet the practice, however, in discussing the stereochemistry in coordination and inorganic chemistry. In the context of coordination and inorganic chemistry, stereochemical information is either presented in the more traditional terminology, or more often by means of a stereospecific structural representation. 

For compounds for which X-ray data have not yet been obtained, generic structural representations are shown. For these reagents, traditional nomenclature, such as uronium salts, has arbitrarily been retained. 

Unambiguous, accurate graphical representation of the stereochemistry of chemical structures is essential. To this end, a task group in the lUPAC Chemical Nomenclature and Structure Representation Division prepared a document that specifies preferred, acceptable, and not acceptable graphical representations for a wide variety of structures. In Figure 2.2, representation 3a is considered acceptable, but 3b is preferred. However, structure 3f (Figure 2.3) is considered not acceptable. 

To describe polymers or polymer blends with greater precision, the qualifiers listed in Table 1.6 have been suggested (Jenkins et al. 1993). In a series of four papers, Wilks (1997a-d) has compared the polymer nomenclature styles and structure representation systems used by Chemical Abstracts Service (CAS), the lUPAC, and MDL Information Systems, Inc. (MDL). 

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