Line notation identifiers

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. 

The Pesticide Index (ref. 14) lists the following categories of pesticides acaricides, attractants, chemosterilants, defoliants, fungicides, herbicides, insecticides, molluscicides, nematicides, plant regulators, repellents, and rodenticides. Listings are in alphabetical order with structural and molecular formulae for single chemical entities. Other data include CAS nomenclature and number Wiswesser Line Notation LD-50 and test animal data when available physical appearance and safety information. Also provided are a CAS nomenclature index separate molecular (line) formulae of chemicals identified by their common names a separate section of Wiswesser line notations, also with common names an appendix of manufacturers, and an appendix of recent publications dealing with pesticide names. 

The most commonly used identifiers today include line notation identifiers (e.g., Simplified Molecular Input Line Entry System [SMILES] and International Chemical Identifier [InChls]), tabular identifiers (e.g., Molfile and Structure Definition [SD] file types), and portable mark-up language identifiers (e.g., Chemical Markup Language [CML] and FlexMol). Each identifier has its strengths and weaknesses as detailed in Chapter 5. Chapters 5 and 6 provide enough information to guide researchers in choosing the most appropriate formats for their individual use. 

These identifiers were developed as an lUPAC project in 2000-2004. They are the most recent technology aimed at an unambiguous text-string representation of chemical structures. (Earlier technologies included Wiswesser line notation, which is not described here, and SMILES, described below.)... 

The lUPAC International Chemical Identifier (InChl) is a relatively recent arrival on the chemical structure representation scene, and combines some of the characteristics of connection table, line notation and registry number identifier. A comprehensive technical description has yet to be published, though substantial details are given in the documentation which accompanies the open-source software provided by lUPAC, and a number of authors have provided good overviews. " ... 

Chemical names are usually used for documentation and communication purposes. A molecule can have several valid chemical names including computer-generated International Union of Pure and Applied Chemistry (lUPAC) names, traditional name, common name, commercial name, company assigned identifiers. Chemical Abstracts Service (CAS) Registry number, and many other synonyms. It is challenging to generate chemical stractures from the chemical names. In order to communicate effectively, line notations were developed for representing chemical struc-... 

All common identifiers such as name, synonyms, CAS Registry Number, molecular formula, molecular weight, Wiss-wesser Line Notation, RTECS, RCRA, and DOT identification numbers, and Standard Tariff Commodity Code (STCC) are included for almost every chemical. The data in CHEMTOX are taken from lists published in the U.S. Federal Register and the Code of Federal Regulations, U.S. government publications, core journals, books, technical reports, and manufacturers safety data sheets. 

Semantic rules are expressed as templates a dialect contains nested packages for its semantic rules. Each rule translates a slightly higher-level notation into its equivalent lower-level one. Here, any line between two type boxes that contains an explicit stereotype means the same as inverse attributes (see Figure 9.41). So what should an association line mean if it has no stereotype tag To define a default, you identify the untagged feature with the appropriate tag9 (see Figure 9.42). 

The index number refers to the principal quantum number and corresponds to the K shell designation often used for the electron of the normal hydrogen atom. The principal quantum number 2 corresponds to the L shell, 3 to the M shell, and so on. The notation s (also p, cl, f to come later) has been carried over from the early days of atomic spectroscopy and was derived from descriptions of spectroscopic lines as sharp, principal, diffuse, and fundamental, which once were used to identify transitions from particular atomic states. 

Fig. 13. Qualitalive fluorescence yields of Parmenter and Schuyler from single vibronic levels of benzene vapor. The solid lines indicate the levels from which moderate to strong fluorescence has been observed when they are individually excited with pressures low enough (ca. 0.2 torr) to preclude significant collisional deactivation prior to electronic decay. The dashed lines indicate levels from which emission was too weak to be observed. The notation on the right identifies the vibrational level. For example, (2 X 6) + 1 indicates emission from the vibrational level (2v + of the state.

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