Notation line structure

Figure 6-1. Different forms of representation of a chemical graph a) labeled (numbered) graph b) adjacency matrix c) connectivity table, type I d) connectivity table, type II f) line notations g) structural index.

Fig. 3 Representation of Lewis structures based on the attainment of closed shells by electron-pair sharing. The initial dot structures have been progressively replaced by line structures to represent the two-electron two-centre bonds. Dots are only retained when they have stereochemical consequences or are required to represent organic reactions using the curly arrow notation (see Fig. 4)...

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 first line notations were conceived before the advent of computers. Soon it was realized that the compactness of such a notation was well suited to be handled by computers, because file storage space was expensive at that time. The heyday of line notations were between I960 and 1970, A chemist, trained in this line notation. could enter the code of large molecules faster than with a structure-editing program,... 

The Wiswesser Line Notation (WLN) was introduced in 1946, in order to organize and to systematically describe the cornucopia of compounds in a more concise manner. A line notation represents a chemical structure by an alphanumeric sequence, which significantly simplifies the processing by the computer [9-11], (n many cases the WLN uses the standard symbols for the chemical elements. Additionally, functional groups, ring systems, positions of ring substituents, and posi-... 

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 1986, David Weininger created the SMILES Simplified Molecular Input Line Entry System) notation at the US Environmental Research Laboratory, USEPA, Duluth, MN, for chemical data processing. The chemical structure information is highly compressed and simplified in this notation. The flexible, easy to learn language describes chemical structures as a line notation [20, 21]. The SMILES language has found widespread distribution as a universal chemical nomenclature... 

HvaluaMon of line notations for representing u chemical structure. 

Chemical structures can be transformed into a language for computer representation via line notations such as ROSDAL, SMILES, Sybyl. 

Stereochemistry can be represented graphically in 2D structures, but also by (permutations) descriptors. It is included in all line notations and exchange formats. 

The problem of perception complete structures is related to the problem of their representation, for which the basic requirements are to represent as much as possible the functionality of the structure, to be unique, and to allow the restoration of the structure. Various approaches have been devised to this end. They comprise the use of molecular formulas, molecular weights, trade and/or trivial names, various line notations, registry numbers, constitutional diagrams 2D representations), atom coordinates (2D or 3D representations), topological indices, hash codes, and others (see Chapter 2). 

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... 

FIGURE 11.18 Furanoses are represented by lines phosphodiesters are represented by diagonal slashes in this shorthand notation for nucleic acid structures. 

Chemists use a special notation to specify the structure of electrode compartments in a galvanic cell. The two electrodes in the Daniell cell, for instance, are denoted Zn(s) Zn2+(aq) and Cu2+(aq) Cu(s). Each vertical line represents an interface between phases—in this case, between solid metal and ions in solution in the order reactant product. 

Chemical identity may appear to present a trivial problem, but most chemicals have several names, and subtle differences between isomers (e.g., cis and trans) may be ignored. The most commonly accepted identifiers are the IUPAC name and the Chemical Abstracts System (CAS) number. More recently, methods have been sought of expressing the structure in line notation form so that computer entry of a series of symbols can be used to define a three-dimensional structure. For environmental purposes the SMILES (Simplified Molecular Identification and Line Entry System, Anderson et al. 1987) is favored, but the Wismesser Line Notation is also quite widely used. 

Anderson, E., Veith, G. D., Weininger, D. (1987) SMILES A Line Notation and Computerized Interpreter for Chemical Structures. EPA Environmental Research Brief, U.S. EPA, EPA/600/M-87/021. 

It has become increasingly popular to represent [C5H5]- by the structure shown in Fig. 6d. This representation is a valence bond structure notation it is intended to represent the five equivalent resonance structures (three of these are shown as Figs. 6c, /, and g the other two are similar), in which the negative charge is located at each carbon in turn. Each double bond is thus only a partial double bond and, if the usual notation of writing a partial double bond by a dashed line were applied, the structure would be written as 6h. The solid circle (6d) is a rapid way to write the 66 structure. In a completely analogous... 

Many researchers have recognized the importance of having an unambiguous grammar for chemical notation, but they have mainly applied WLN [8] to on-line compound search [9] and structural summary (identification of common structural features) [10]. Johns and Clare point out that it is a linguistic rather than merely a symbolic notation. This means that the symbols are represented and manipulated in well defined structures. This section relies on the unambiguousness of WLN to recognize parent molecules while Section 5 relies on the WLN rules to actually manipulate symbol structures. 

Fritts, Lois E., Margaret Mary Schwind, Using the Wiswesser Line Notation (WLN) for Online, Interactive Searching of Chemical Structures, J. Chem. Inf. Comput. Sci., 22, (1982), pp. 106-109. 

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