Chemical structure, representation

A connection table has been the predominant form of chemical structure representation in computer systems since the early 1980s and it is an alternative way of representing a molecular graph. Graph theory methods can equally well be applied to connection table representations of a molecule. 

Walking through the Hierarchy of Chemical Structure Representation... 

Thorner, D.A., Willett, P., Weight, P.M., and Taylor, R. Similarity searching in files of three-dimensional chemical structures Representation and searching of molecular electrostatic potentials using field-graphs./. Comput.-Aided Mol. Des. 1997, 3 3, 163-174. 

Fig. 9.6 Human versus machine-readable chemical structure representations. Names based on the depicted structures were interpreted using ACDName [22]. The cross up/down wedge error (middle) causes errors in assigning the absolute chirality.

Computer-Aided Property Estimation Computer-aided structure estimation requires the structure of the chemical compounds to be encoded in a computer-readable language. Computers most efficiently process linear strings of data, and hence linear notation systems were developed for chemical structure representation. Several such systems have been described in the literature. SMILES, the Simplified Molecular Input Line Entry System, by Weininger and collaborators [2-4], has found wide acceptance and is being used in the Toolkit. Here, only a brief summary of SMILES rules is given. A more detailed description, together with a tutorial and examples, is given in Appendix A. 

The chemical business rules of a compound registration solution define the individual identities of chemical structure representations in order to meaningfully assign a unique corporate ID to each unique structure. After applying these rules, standardized parent structures are stored in a main structure table. The (structure) records from the original compound library data file entering the system are saved into a batch table on which each batch entry is associated with its unique parent structure. All data relating to the physical compound sample remain uniquely associated with this batch entry and thus are also associated with one unique parent structure. 

The conversion of chemical names and identihers into appropriate chemical structure representations offers the ideal path for chemists and organizations to mine chemical information. Because chemical names are not unique and a multitude of labels can map to a single chemical entity, the facile conversion of alphanumeric text identihers to a connection table representation enables superior data capture, representation, indexing, and mining. The industry s need to mine more information from both the historical corpus as well as new sources is obvious, and a number of researchers have initiated research into the domain of chemical identiher text mining and conversion. Multiple efforts have been made in the held of bioinformatics research,8 and, while interesting as a parallel, in this chapter we will focus the efforts to extract and convert identihers related to chemical entities rather than, for example, genes, enzymes, or proteins. 

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. 

Ash, S., M.A. Cline, R. Webster Homer, T. Hurst, and G.B. Smith. 1997. SYBYL Line Notation (SLN) a versatile language for chemical structure representation. J. Chem. Inf. Comput. Sci. 37 71-79. 

Chemical structure representation formats (e.g., InChl, Simplified Molecular Line Entry System [SMILES])... 

Stein, S. E., Heller, S. R., Tchekhovski, D. An open standard for chemical structure representation the lUPAC chemical identifier. Proceedings of the 2003 International Chemical Information Conference (Nimes, France), Infonortics, 2003, pp. 131-143. 

Adjacency Matrix is a chemical structure representation in a matrix consisting of binary components that indicate whether two atoms are bonded or not. 

The chemical structure representation in Apex-3D is based on the concept of a descriptor center that represents a part of the hypothetical biophore. Descriptor centers can be atoms, sets of atoms, pseudo-atoms, or substructures that participate in ligand-receptor interactions. The interaction is derived from electrostatic, hydrophobic, dispersion force, and charge-transfer information that comes from quantum-chemical calculations or from atomic conkibutions to hydrophobicity or molar refractivity. 

Any representation of chemical structure is thus a complex cipher, allowing our model of structure such brevity as to mask the distinction between the model and the reality of chemical structure. The foregoing evolution of such representations is a testament to both our evolving understanding of structure and the human capacity for encoding any information. In this latter sense, however, chemical structure representation is quite naturally suited to the computer age. 

Fliri, A., Moysan, E., Benichou, P., and Nolle, M. (2009) Methods for processing generic chemical structure representations. Patent W009051741. 

Two important characteristics of a chemical structure representation are the extent to which it provides an unambiguous representation of the structure i.e. whether or not the representation corresponds to a single chemical entity), and whether or not it is a unique, or canonical , representation of the structure i.e. if there is only one correct representation of this type for a particular chemical entity). The question of unambiguity depends on the definition of a... 

Computer representations of chemical structures have evolved over several decades, and continue to do so as new and possibly, though not necessarily, improved formats achieve popularity or market penetration. There are a number of general discussions on chemical structure representations, both in textbooks and in review articles . This section attempts to provide an up-to-date summary of those currently considered most important, in an historical context. 

The lUPAC International Chemical Identifier (InChl) is a relatively recent arrival on the chemical structure representation scene, and combines some of the characteristics of connection table, line notation and registry number identifier. A comprehensive technical description has yet to be published, though substantial details are given in the documentation which accompanies the open-source software provided by lUPAC, and a number of authors have provided good overviews. " ... 

Topological graphs are concerned only with which nodes (atoms) are joined by which edges (bonds), thus have difficulty in representing stereochemistry directly. A number of approaches have been used to incorporate information about stereochemical configuration into chemical structure representations. ... 

Figure 16.13 Chemical structure representation of the synthesized poly(dimethylsiloxane)...

Infrared and Raman spectra, both scaled to the most intensive bands, are presented as stack-plots in the region 4000-100 cm. The absorbance scale is more suitable for comparison of relative band intensities in the IR and Raman spectra. On the other hand, in most IR atlases the spectra are presented using the transmittance scale this includes the only atlas of combined IR and Raman spectra [59] which uses the central part of the page, between the spectra, for chemical structure representation. Thus the conventional transmittance scale was chosen as it is more suitable for rational distribution of information in the combined figure and for an easier comparison by the reader of presented IR spectra with other well-known reference collections. 

The idea of using symbol frequencies to guide the selection of an indexing vocabulary for search in the two-dimensional domain of chemical structure representations then prompted us to look at the applicability of these ideas in the text processing context - an example of phenomenon - driven research. This led to a series of studies of the... 

Fisanick, W. Storage and Retrieval of Generic Chemical Structure Representations by Computer. U.S. patent US 4,642,762A, 10 Feb 1987. 

Substructure searching is the process of searching a file of chemical structure representations, not to find a particular compound, but to find any and all compounds which contain the same specified query substructure. 

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