SMILES line system

SMILES (Simplified Molecular Input Line Systems), 6 3-6 Smith, Adam, 24 364 Smith—Ewart kinetics, 14 715 Smith-Ewart recursion formula, 14 715 Smith-Ewart theory, 25 571, 572 VDC polymerization and, 25 697... 

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... 

SMILES Simplified Molecular Input Line Entry System... 

For each selected PFC, a profile was edited including the name of the compound, its CAS (Chemical Abstracts Service) number and the SMILES (Simplified Molecular Input Line Entry System) formula. 

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. 

Toropov AA, Toropova AP, Mukhamedzhanova D, Gutman I (2005a) Simplified molecular input line entry system (SMILES) as an alternative for constructing quantitative structure-property relationships (QSPR). Indian J. Chem. Sect A. 44 1545-1552. 

Table 1 shows an example of markup, generated using the OSCAR 3 system. The abstract of a polymer research paper has been parsed by OSCAR and the resulting markup for the first sentence of the abstract is shown in-line with the text (Table IB). The first chemical entity encountered in the sentence is oleic acid , which has been marked up as type = CM (Chemical Moiety) and a number of other annotations, such as in-line representations of chemical structure (InChl, SMILES) have been attached. 

SMILES (Simplified Molecular Input Line Entry Systems) is a line notation system based on principles of molecular graph theory for entering and representing molecules and reactions in computer (10-13). It uses a set of simple specification rules to derive a SMILES string for a given molecular structure (or more precisely, a molecular graph). A simplified set of rules is as follows ... 

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. 

The Simplified Molecular Input Line Entry System (SMILES) is frequently used for computer-aided evaluation of molecular structures [1-3]. SMILES is widely accepted and computationally efficient because SMILES uses atomic symbols and a set of intuitive rules. Before presenting examples, the basic rules needed to enter molecular structures as SMILES notation are given. 

In addition to these publications, software is available that allows the user to determine vapor pressures of a wide variety of compounds at room temperature. The Texas Research Center (TRC) (1996) distributes a PC DOS/Windows database that contains experimentally derived Antoine constants for approximately 6000 chemicals from which vapor pressures at user-selected temperatures can be calculated. Another Windows-based program, MPBPVP by Meylan and Howard (1996), estimates the vapor pressure of organic compounds from their SMILES (Simplified Molecular Input Line Entry System) structure and their boiling points using the Antoine equation, the Grain-Watson method, and the Mackay method. 

For abbreviation of analyte names see Sect. Abbreviations , log P logarithm of octanol/water partition coefficient n.c. not calculable as N-atom of tropane moiety is present as alkylated quaternary amine, pKb negative decadal logarithm of base constant, SMILES simplified molecular input line entry system... 

Imports data in SD file format, MDL molfile format, SMILES text strings, Daylight Chemical Information Systems Inc. s Thor Data Tree (TDT) format, and Tripos Inc. s Sybyl Line Notation (SLN) format. 

As described in Chapter 9 there are an increasing number of commercial toxicological prediction systems available. Naturally these have been designed to be user friendly most run under Microsoft Windows and use the Simplified Molecular Input Line Entry System (SMILES) as the molecular input. It is therefore possible to obtain a prediction of toxicity instantaneously, and often this may be performed for large numbers of compounds. There is a great temptation to use predicted toxicities at face value (i.e., if a compound is predicted to be non-toxic then it must be non-toxic). This simplistic use of predicted values should be avoided at all costs. Ideally, there are a number of criteria that should be applied when predicting toxicity. It is essential that a trained expert uses the predictive system. The user should be an expert both in the endpoint being predicted and the use of the predictive system. 

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. 

Devillers et al. (1996) have commented that most QSARs for the prediction of BCF perform similarly up to log Kow 6. In view of the fact that the computer program BCFWIN version 2.14 is freely available from the EPA website (www.epa.gov/oppt/exposure/docs/episuitedl.htm), it is recommended that this be used for BCF prediction for chemicals with log < 6 the proviso is that highly reactive chemicals will probably have a higher than predicted BCF, perhaps by up to two orders of magnitude. BCFWIN requires that the chemical structure be input using Simplified Molecular Line Entry System (SMILES) notation (Weininger, 1988) or as a Chemical Abstracts Service (CAS) number. 

SMILES simplified molecular input line entry system http //www.daylight.com/smiles/index.html. National Institutes of Health Assay Guidance Manual Version 5.0 http //www.ncgc.nih.gov/guid-ance/manual toc.html. 

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. 

---