Chemical notations

On this see, Timothy L. Albom, "Negotiating Notation Chemical Symbols and British Society,... 

Graph-theoretical notion Notation Chemical notion Notation Type of information... 

Cal ratio Chemical formula Cement chemical notation Chemical name (IUPAC notation) Common acronyms... 

Structure Notation Chemical shifts (ppm down-fieid from TMS) ... 

Chemical Formula Shorthand Notation Chemical Name Weight Percent... 

E. G. Smith and P. A. Baker, The Wiswesser Line-Formula Chemical Notation , Chemical Information Management, Cherry Hill, NJ, 1975. 

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. 

A completely difierent approach to scattering involves writing down an expression that can be used to obtain S directly from the wavefunction, and which is stationary with respect to small errors in die waveftmction. In this case one can obtain the scattering matrix element by variational theory. A recent review of this topic has been given by Miller [32]. There are many different expressions that give S as a ftmctional of the wavefunction and, therefore, there are many different variational theories. This section describes the Kohn variational theory, which has proven particularly useftil in many applications in chemical reaction dynamics. To keep the derivation as simple as possible, we restrict our consideration to potentials of die type plotted in figure A3.11.1(c) where the waveftmcfton vanishes in the limit of v -oo, and where the Smatrix is a scalar property so we can drop the matrix notation. 

The index J can label quantum states of the same or different chemical species. Equation (A3.13.20) corresponds to a generally stiff initial value problem [42, 43]. In matrix notation one may write ... 

In chemistry, chemical structures have to be represented in machine-readable form by scientific, artificial languages (see Figure 2-2). Four basic approaches are introduced in the following sections trivial nomenclature systematic nomenclature chemical notation and mathematical notation of chemical structures. 

Before discussing the different ways of representing a chemical compound, some terms have to be defined concerning the reproducibility or transformation of structures and notations. 

The major significance of chemical nomenclature or notation systems is that they denote compounds in order to reproduce and transfer them from one coding to another, according to the intended application. As each coding may not include all the pieces of information in the other coding, or may have interpre table coding rules, the transformation is not always unambiguous and unique. 

The systematic lUPAC nomenclature of compounds tries to characterize compounds by a unique name. The names are quite often not as compact as the trivial names, which are short and simple to memorize. In fact, the lUPAC name can be quite long and cumbersome. This is one reason why trivial names are still heavily used today. The basic aim of the lUPAC nomenclature is to describe particular parts of the structure (fi agments) in a systematic manner, with special expressions from a vocabulary of terms. Therefore, the systematic nomenclature can be, and is, used in database systems such as the Chemical Abstracts Service (see Section 5.4) as index for chemical structures. However, this notation does not directly allow the extraction of additional information about the molecule, such as bond orders or molecular weight. 

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 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 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 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... 

SLN is easy to learn and its use is intuitive. The language uses only six basic components to specify chemical structures. Four of them are hsted in Table 2-3 and can be compared directly with the SMILES notation of Section 2,3.3. 

HvaluaMon of line notations for representing u chemical structure. 

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)... 

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

W.J. Wiswesser, A Line-Formula Chemical Notation, Y. Thomas Crowell, New York, 1954. 

E.G. Smith, The Wisivesser Line-Formula Chemical Notation, McGraw-Hill,... 

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. 

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.

Fischer projections and d-l notation have proved to be so helpful m representing carbohydrate stereochemistry that the chemical and biochemical literature is replete with their use To read that literature you need to be acquainted with these devices as well as the more modern Cahn-Ingold-Prelog R S system... 

The lattice model that served as the basis for calculating ASj in the last section continues to characterize the Flory-Huggins theory in the development of an expression for AHj . Specifically, we are concerned with the change in enthalpy which occurs when one species is replaced by another in adjacent lattice sites. The situation can be represented in the notation of a chemical reaction ... 

Chemical Properties. The notation used by Chemical Abstracts to reflect the configuration of tartaric acid is as follows (R-R, R )-tartaric acid [S7-69A-] (4) (S-R, R )-tartaric acid [147-71-7] (5) and y j O-tartaric acid [147-73-9] (6). Racemic acid is an equimolar mixture of the two optically active enantiomers and, hence, like the meso acid, is optically inactive. 

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