Line notations

In this notation the chemical symbols are written on one line using the normal atomic symbols and relevant subscripts or superscripts. Each element is bonded directly to the one to the left, unless all the valences of that atom are satisfied, in which case it is bonded to the next one to the left, and so on as necessary. 

Parentheses may be used to avoid ambiguities. Abbreviations may be used for common groups when certain points need to be highlighted. 

This method is useful for portraying chemical formulae in typescripts and manuscripts, as a lot of information is conveyed in a condensed manner. However, it suffers from the problem that it does not give a pictorial representation of the stereochemistry of the molecule. In order to overcome this deficiency, it is possible to include the appropriate Cahn-Ingold-Prelog prefix, namely R or S, to indicate diastereo details, or one of the cis, trans, ortho, meta or para prefixes to indicate geometrical details.  

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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. 

WLN Wiswesser line notation, wolfram An alternative name for tungsten. 

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,... 

In Sections 2,.3.1-2.3.4, only the four most popular line notations, Wiswesser (WLN), ROSDAL. SMILES, and Sybyl (SEN), arc discussed. Whereas WLN is now almost obsolete, SMILES is quite an important representation and is widely used (Figure 2-7). 

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). 

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.

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... 

Topological indices are used to describe some components of connectivity. A more complete description is afforded by unidimensional codes (linear line notations) such as SMILES. Connectivity plus explicit attention to valence electrons is afforded by the electrotopological indices... 

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. 

The above is based on the calculation of a collective r for the whole molecule. This value changes the HOMO of either the diene or dienophile, as is necessary. This equation is accurate to about 0.5 eV on either side of the known values [15]. The value of ttotal is inserted into the HOMO-LUMO calculation as the parameter r Y), Note that in its pure form, this equation only yields values for the HOMO orbitals. Corrections are used for the calculation of the LUMO values. Table 1 contains examples of the Wiswesser Line Notation and the raw r values used in the computation of orbital energies. 

General forms are easily developed for other reactions. The machinery introduced in this section can then be utilized to write disconnection rules for other reactions. For example, consider the Diels-Alder adduct bicyclo[2.2.1]hept-2-ene. Using the regular expression notation described previously, the line notation for these types of compounds can be represented as... 

There are several future research directions for this project. First, results from the FMO reaction check are not infallible due to the qualitative nature of this check. A more precise, yet computationally feasible model may be possible. Second, more work remains in the WLN rearranger a full system based on our concepts would require knowledge of the entire complement of WLN rules. It may also be desirable to adopt or develop another, more computationally tractable line notation for the purpose of synthetic analysis. Finally, we would like to extend our work to more reaction classes to examine its potential in more detail. 

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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