Nomenclature Software

Eller, G. A. 2006. Improving the quality of published chemical names with nomenclature software. Molecules, 11 915-928. 

The commercial 2D structure editor. Chemistry 4D-Draw, from Chemlnnovativc Software Inc., includes two additional special modules besides conventional chemical drawing tools. NamExpert provides the interpretation ofa compound name according to the lUPAC nomenclature to create the corresponding chemical structure. The latter can be represented in three different styles the shorthand. Kckulc. or semi-structural formula. In contrast to NamExpert, the Nomenclature module assigns lUPAC names to drawn structures. 

Structure and Nomenclature Search System. This system links the collection of chemical databases found in the Chemical Information System (CIS), one of the first interactive systems for stmcture and substmcture searching. References from the separate files can be retrieved by SANSS using CAS Registry Numbers, and the database of stmctures may be searched for stmctures or substmctures. An adaptation of the SANSS software for substmcture searching has been incorporated in the Dmg Information System of the National Cancer Institute for its own use (54). 

Each simulation example is identified by a file name and title, and each comprises the qualitative physical description with drawing, the model equation development, the nomenclature, the ISIM program, suggested exercises, sample graphical results and literature references. The diskette in the pocket at the back of the book contains the programs and the ISIM software. 

MDL Information Services, Inc. offers free software downloads at http // www.mdli.com/cgi/dynamic/downloadsect.html7uid= key= id = 1. These include AutoNom Standard (automatic nomenclature), which generates IUPAC chemical names directly from graphical structures created in ISIS/Draw or registered in ISIS/ Base. 

Nomenclature resources help the user give correct names to chemical structures. Visualization resources allow the user to build molecules from scratch or display molecular structures imported from databases or other software programs (like the Protein Data Bank, PDB, for example). 

PHYSICAL ORGANIC CHEMISTRY NOMENCLATURE MARQUARDT ALGORITHM COMRUTER ALGORITHMS SOFTWARE MASS-ACTION RATIO Mass-action ratio, determination,... 

We close this section with one more note on careful nomenclature. A code renders a model into a set of instructions that can be understood by a digital computer. Thus, if one applies a particular model, let us say the molecular mechanics model called MM3 (which will be described in the next chapter) to a particular problem, say the energy of chair cyclohexane, the results should be completely independent of which code one employs to carry out the calculation. If two pieces of software (let s call them MyProg and YourProg) differ by more than the numerical noise that can arise because of different round-off conventions with different computer chips (or having set different tolerances for what constitutes a converged calculation) then one (or both ) of those pieces of software is incorrect. In colloquial tenns, there is a bug in the incorrect code(s). 

II. Product Summaries Cheminnovation Software, Inc provides software for chemistry graphics, molecular modeling, chemical nomenclature, and chemical and biological information management through the Internet. Products include ... 

Our intention in this chapter is to examine the challenges of extracting identihers from chemistry-related documents and the conversion of those identihers into chemical structures. The authors of this work each have well over a decade of experience in chemical structure representation and systematic nomenclature. We have been deeply involved in the development of software algorithms and software for the generation of systematic names and the conversion of chemical identihers into chemical structures.9 Although we have our own biases concerning approaches to the problem of N2S conversion, we have done our utmost to be objective in our review of the subject and comparison of approaches and performance. 

Chemical nomenclature has a very large number of specific procedures to create chemical names, and many of these are not easily amenable to algorithmic representation, requiring significant investments in both development and validation time to develop automated procedures. Software developers of N2S engines prefer to support just the basic operations for conversion, at least at the early stages of development. 

Nomenclature for the eight-membered 1,4-diheterocycles follows ILJPAG rules and the names are generated with the ACD software. The parent unsaturated systems are referred to as the corresponding -cines, whereas the fully saturated rings are recognized as -canes. Benzo and dibenzo derivatives follow the standard IUPAC nomenclature. Specific names appear for the individual compounds, where appropriate. 

Ambiguous version nnmbering nomenclatures, particularly for software where media might be labeled by date rather than by the version of the software carried... 

A special attention is given to stereochemistry, as some compounds are published without proper chirality representation even though the information is available, for example, for natural compounds and their derivatives. Furthermore, as illustrated in Fig. 13.2-8, compounds published in medicinal chemistry literature are often depicted in a human-readable format that is, structures are drawn in a format that chemists can interpret to reconstruct proper chirality. However, this format is not machine-readable , that is, cheminformatics software for 3D structural conversion, or for automatically generating IUPAC (International Union of Pure and Applied Chemistry) nomenclature, cannot perceive the stereo centers correctly... 

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