Linear structural notation

Figure 2a. Context Free structural grammar for computer input of linear structure notation via teletype. Meanings of nontermirml symbols are as above.

The ROSDAL syntax is characterized by a simple coding of a chemical structure using alphanumeric symbols which can easily be learned by a chemist [14]. In the linear structure representation, each atom of the structure is arbitrarily assigned a unique number, except for the hydrogen atoms. Carbon atoms are shown in the notation only by digits. The other types of atoms carry, in addition, their atomic symbol. In order to describe the bonds between atoms, bond symbols are inserted between the atom numbers. Branches are marked and separated from the other parts of the code by commas [15, 16] (Figure 2-9). The ROSDAL linear notation is rmambiguous but not unique. 

In order to calculate a physicochemical property, the structure of a molecule must be entered in some manner into an algorithm. Chemical structure notations for input of molecules into calculation software are described in Chapter 2, Section VII and may be considered as either being a 2D string, a 2D representation of the structure, or (very occasionally) a 3D representation of the structure. Of this variety of methods, the simplicity and elegance of the 2D linear molecular representation known as the Simplified Molecular Line Entry System (SMILES) stands out. Many of the packages that calculate physicochemical descriptors use the SMILES chemical notation system, or some variant of it, as the means of structure input. The use of SMILES is well described in Chapter 2, Section VII.B, and by Weininger (1988). There is also an excellent tutorial on the use of SMILES at www.daylight.com/dayhtml/smiles/smiles-intro.html. 

There are several linear canonical notations for the input of chemical structures into the computer notable among these are the Wiswesser line notation [226] and the IUPAC notation [227], which are used in industrial information systems. In order to achieve a canonical notation, a large number of rules are necessary, more than three hundred in the Wiswesser line notation [226]. Furthermore, the resulting notation is quite arbitrary and very far from the usual practice of a chemist for example, acetone is 1V1 in the Wiswesser notation. In conclusion, both coding a formula and reading a coded formula in the Wiswesser notation require highly trained chemists. 

The effective communication of chemical structure is essential for all chemists. Over the years many different types of structure representation have been developed. Before the use of computers, chemists drew structures manually, often using a linear text notation. As more sophisticated methods for drawing have become available, the trend has been toward two-dimensional stick structures, such as the zigzag Natta projection (Figure 8.1). 

NUMERIC CODE NOTATION FOR THE MEMBERS OF LINEAR STRUCTURE SERIES... 

Wiswesser line notation The Wiswesser line-formula notation (WLN) is a method for expressing the more usual graphical structure of a chemical compound as a linear string of symbols. The resulting alternative notation is unambiguous, short and particularly suitable for computer processing and retrieval but can also be understood easily by chemists after minimal training in its use. 

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 ROSDAL (Representation of Organic Structures Description Arranged Linearly) syntax was developed by S. Welford, J. Barnard, and M.F. Lynch in 1985 for the Beilstein Institute. This line notation was intended to transmit structural information between the user and the Beilstein DIALOG system (Beilstein-Ohlme) during database retrieval queries and structure displays. This exchange of structure information by the ROSDAL ASCII character string is very fast. 

In contrast to canonical linear notations and connection tables (see Sections 2.3 and 2.4), fragment codes arc ambiguous. Several different structures could all possess an identical fragment code, because the code docs not describe how the fragments arc interconnected. Moreover, it is not always evident to the user whether all possible fi aginents of the stmetures ai e at all accessible. Thus, the fragments more or less characterise a class of molecules this is also important in generic structures that arise in chemical patents (sec Section 2.7.1)... 

An alternative way to represent molecules is to use a linear notation. A linear notation uses alphanumeric characters to code the molecular structure. These have the advantage of being much more compact than the connection table and so can be particularly useful for transmif-ting information about large numbers of molecules. The most famous of the early line notations is the Wiswesser line notation [Wiswesser 1954] the-SMILES notation is a more recent example that is increasingly popular [Weininger 1988]. To construct the Wiswesser... 

Of course, in reactions (5.A) and (5.B) the hydrocarbon sequences R and R can be the same or different, contain any number of carbon atoms, be linear or cyclic, and so on. Likewise, the general reactions (5.C) and (5.E) certainly involve hydrocarbon sequences between the reactive groups A and B. The notation involved in these latter reactions is particularly convenient, however, and we shall use it extensively in this chapter. It will become clear as we proceed that the stoichiometric proportions of reactive groups-A and B in the above notation—play an important role in determining the characteristics of the polymeric product. Accordingly, we shall confine our discussions for the present to reactions of the type given by (5.E), since equimolar proportions of A and B are assured by the structure of this monomer. 

Four main approaches have been suggested for the representation of chemical structures in machine-readable form fragment codes, systematic nomenclature, linear notations, and connection tables. 

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... 

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