Chemical documentation representations

In the AC-matrices the off-diagonal entries ey are the formal bond orders between atom pairs (Aj, A/). BE-matrices are obtained from the AC-matrices by augmentation with diagonal entries eu indicating the numbers of free valence electrons at the atoms Aj. The indices 1,. .., n can be assigned to the n atoms of a constitution in n different ways. Accordingly there are up to n different but equivalent connectivity lists, or AC- and BE-matrices, respectively. The direct identification and comparison of such representations is essential to Chemical Documentation. Only by uniquely assigning atomic indices can this be accomplished. 

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. 

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. " ... 

That economics played a role early on at Searle was mentioned in a paper my predecessor Dr. Howard Bonnett wrote in the Journal of Chemical Documentation in 1962 ( 3). Work was being done at that time on computer representation of 2-D chemical graphics, but it required prohibitively expensive, single application, equipment. He noted that one of the primary reasons Searle had adopted Wiswesser Line Notation was that the notation could be used on a standard accounting computer and did not require a high capital outlay. 

Because chemical structure representation in diagrammatic form has inconsistencies and contradictions built into it, it is impossible to anticipate every case. Most of the problem areas can be dealt with by a few general rules, but to cover all eventualities would require a huge system of regulations, with many provisos. Therefore, the aim of our rules is to cover the commonest problems and to ensure that only one representation will need to be assigned in most cases. Even when the rules fail to resolve a choice of structure completely, at least the number of possible structures should be reduced. In cases not covered by our rules, the structures given in the document will be indexed. 

In the second group are two distance matrices the first has been known in physics [18] and the second in mathematics [19-21] and mathematical chemistry [22-28], The last matrix is a newly modified terminal matrix, to be explained shortly, which offers highly compact matrix representation of polycyclic molecules and may be of potential interest in chemical documentation. 

In a chemical documentation system, each substance must be characterized by a unique name. This unique name is used for storage, retrieval, and comparison of che-mical compounds. The nomenclature systems used by humans to communicate chemical information are not fit for computer manipulation, and special chemical structure representations are developed for chemical database management and searching (see Structure and Substructure Searching and Structure Databases). 

GORE. The CORE Electronic Chemistry Library is a joint project of Cornell University, OCLC (On-line Computer Library Center), Bell Communications Research (Bellcore), and the American Chemical Society. The CORE database will contain the full text of American Chemical Society Journals from 1980, associated information from Chemical Abstracts Service, and selected reference texts. It will provide machine-readable text that can be searched and displayed, graphical representations of equations and figures, and full-page document images. The project will examine the performance obtained by the use of a traditional printed index as compared with a hypertext system (SUPERBOOK) and a document retrieval system (Pixlook) (6,116). 

It is sincerely hoped that the information presented in this document will lead to an even more impressive record for the entire industry however, the American Institute of Chemical Engineers, its consultants, CCPS Subcommittee members, their employers, their employers officers and directors, and Arthur D. Little, Inc., disclaim making or giving any warranties or representations, express or implied, including with respect to fitness, intended purpose, use or merchantability and/or correctness or accuracy of the content of the information presented in this document. As between (1) American Institute of Chemical Engineers, its consultants, CCPS Subcommittee members, their employers, their employers officers and directors, and Arthur D. Little, Inc., and (2) the user of this document, the user accepts any legal liability or responsibility whatsoever for the consequence of its use or misuse. 

Graphic representations (chemical formulae) of macromolecules are used extensively in the scientific literature on polymers including lUPAC documents on macromolecular nomenclature. This document establishes rules for the unambiguous representation of macromolecules by chemical formulae. The rules apply principally to synthetic macromolecules. Insofar as is possible, these rules are consistent with the formulae given in lUPAC documents [2-4] and they also cover the presentation of formulae for irregular macromolecules [5], copolymer molecules [1, 6] and star macromolecules. 

In comparison with chemical formulae of low-molecular-weight compounds, the graphical representations of which have been addressed in a recent lUPAC document [7], chemical formulae of polymers must additionally reflect the multiplicity of constitutional units in a macromolecule and the various possibilities for connecting the constitutional units in a macromolecule. 

Graphical Representation. Occasionally it is desirable to store chemical structures as "pictures", usually for document purposes. For example, some chemical drawing packages and many molecular modeling packages can store structures as the following ... 

The materials, safety information, and procedures contained in this book are believed to be reliable. This information and these procedures should serve only as a starting point for laboratory practices, and they do not purport to specify minimal legal standards or to represent the policy of the American Chemical Society. No warranty, guarantee, or representation is made by the American Chemical Society as to the accuracy or specificity of the information contained herein, and the American Chemical Society assumes no responsibility in connection therewith. The added safety information is intended to provide basic guidelines for safe practices. Therefore, it cannot be assumed that all necessary warnings and precautionary measures are contained in this document and that other or additional information and measures may not be required. Users of this book and the procedures contained herein should consult the primary literature and other sources of safe laboratory practices for more exhaustive information. 

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