Linear chemical notation

The free radical reactions below have been classified into three main categories those which increase the number of free radicals, those which conserve, and those which decrease the number of free radicals. A two-letter index has been given beside the descriptive term of the reaction which will be used when generating mechanisms. The meaning of the symbols +M and (+M) will be commented on in paragraph 2. The examples are presented with the NANCY linear chemical notation described in the appendix NOTATIONS at the end of the book. 

MULLER C., SCACCHI G., C6ME G.M., A compiler for a linear chemical notation. Comp. Chem., 15, 337 (1991). 

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). 

Briefly, notation systems attempt to record full, multidimensional structural descriptions in a linear form, by the use of more comprehensive symbols than atoms and bonds (e.g. symbols for particular chains, rings, functional groups). Thus, more information is recorded implicitly, in Uie rides of the notation, and less is recorded explicitly in the notations for individual compounds. The rules can therefore be quite complicated, in order to ensure the notations are unique and unambiguous. For the Wiswesser Line Notation, the rules are given in Smith, E. G. The Wis-wesser Line-Formula Chemical Notation. New York McGraw-Hill 1968. In this notation, for example, saturated carbon chains are simply indicated by an arable numeral equal to the number of carbons in the chain, branch-... 

The chemical notation most frequently used in this work is a linear or monodimensional (ID) notationL This type of representation has been chosen as it allows the detailed chemical formulae of the molecules and of the free radicals and the equations of reaction to be conveniently entered into the computer, and also to be printed in the same format. 

There are two principal techniques for representing chemical stmctures in digital databases as coimection tables or adjacency matrices— MDL Molefile, PDB, CML—or as linear string notations—SMILES, SMARTS, WLN, InChl. 

Rules for lUPAC Notation for Organic Compounds (Longmans, 1961) is based on the Dyson system and provides a linear cipher for all chemical substances of known structure which can be adopted for indexes. It supersedes A Proposed International Chemical Notation (1958). Some useful lists of symbols have also been published e.g. the Manual of Physico-chemical Symbols and Terminology (issued separately and in J. Amer. chem. Soc. 82, 5517-22 (1960), and the now out-of-date Symbols of Thermodynamical and Physico-chemical Quantities and Conventions Relating to their Use Chem. Ind. 15, 860-5 (1937) Analyst 62, 800-5 (1937)), and International Physico-chemical Symbols (Z. Elektrochem. 27, 5TI-yi (1921). Another volume in the Advances in Chemistry series. No. 14, Nomenclature for Terpene Hydrocarbons, describes the system approved by the ACS and accepted in part by lUPAC. 

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 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 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)... 

WC. Herndon, Canonical labelling and linear notation for chemical graphs, in Chemical AppUcations of Topology and Graph Theory, R.B. King (Ed.), Elsevier, Amsterdam, 1983, pp. 231-242. 

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. 

Figure 1. Five representations of the same chemical information. The canonical chemical reaction graph (a) can be represented in linear notation (b, see Appendix) or as a bond-centered labeled graph (c) by using time-variant bonds. The labeled graph affords an adjacency table (d) and a LISP list representation (e).

The representation is unambiguous since it corresponds to one and only one substance, but it is not unique because alternative numberings of the connection table would result in different representations for the same chemical substance (the connection table representation is discussed in more detail below). In addition to being categorized according to their uniqueness and ambiguity, chemical substance representations commonly used within computer-based systems can be further classified as systematic nomenclature, fragment codes, linear notations, connection tables, and coordinate representations. 

Dittmar, Stobaugh, and Watson [8] describe the connection table utilized in the CAS Chemical Registry System. Lefkowitz [9] describes a concise form of a connection table, called the Mechanical Chemical Code, which does not explicitly identify the bonds and has attributes of both a connection table and linear notation. 

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. 

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. 

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