Structure exchange format

To become familiar with structure exchange formats such as Molfile and SDfile... 

There are many file formats used to store chemistry-specific information. Most have evolved from historical applications without going through a proper design process. They often started as private formats of some program and were reused in other projects. Unfortunately, some of the most established structure exchange formats are also those which lack most in the areas of flexibility and clear coding syntax and are consequently those which are most heavily abused. Some of the major formats are as follows. 

ROSDAL is used in the Beilstein-DIALOG system [17] as a data exchange format. The code can represent not only full structures and substructures but also some generic structures. 

Stereochemistry can be represented graphically in 2D structures, but also by (permutations) descriptors. It is included in all line notations and exchange formats. 

Besides rearrangements, ligand exchange, formation of alkanes, alkenes and other products, release of cyclopropanes is one of the most important reactions of metallacyclobutanes. Of course, this latter reaction is only useful in cyclopropane synthesis if the product is not identical with the starting material used to form the metallacyclobutane. Nevertheless, the discovery of a complex formed from hexachloroplatinic acid and cyclopropane and later structural elucidations have initiated intensive investigations on the conversion of cyclopropanes to metallacyclobutanes and release of cyclopropanes from the latter. These results have been thoroughly discussed in several reviews. " Therefore in this section only some general aspects of cyclopropane formation from metallacyclobutanes and selected synthetically useful methods are discussed. 

Using the XML export function, a work process model can be stored in a structured standard format, which is a universal exchange format for a number of software tools. As XML files can be easily rearranged or altered into a user-defined format by means of XSLT Extensible Stylesheet Language Transformations, [602]), the XML export is useful when WOMS models are to be used by other software applications. Some examples are given in the following subsections. 

The Cell Markup Language [Lloyd, Halstead, and Nielsen 2004] has been under development since 1999 by scientists from the University of Aukland and formerly also Physiome Sciences. It is an open XML-based exchange format for the general description of the structure, mathematics, and state of cellular models. 

The studies of aggregation in polymer systems, association of macromolecules with other molecules, as well as of solubilization, are of extreme importance, since many processes that occur in living organisms (the formation of membranes and cellar structures, exchange processes, enzymatic catalysis, etc.) are all based on these phenomena. 

The basic forms of representation for chemical structures are well established, and although some changes to the details of exchange formats, and the popularity of different ones, remains likely, the principles on which they are constructed will probably remain the same. The changes that are most likely to occur will concern matters such as stereochemistry and aromaticity (and other delocalised bonding patterns) and the point at which differently represented structures are to be regarded as distinct. The problem here is less that new techniques are required and more that none of the established techniques provide the perfect solution. 

Chemisorption of COj leads to carbonate structures. Carbonate formation is accelerated by preadsorbed water (cf. also [543]). According to Boese et al. [608], the assignment of the corresponding bands is difficult because of band overlap. However, the authors tentatively attributed a band pair found with CO2 on Nai jLiio.y-A at 1660 and 1365 cm to a bidentate structure and a second one at 1588 and 1421 cm to a monodentate structure (cf. [543,641]). From alkali ion-exchanged zeolites, carbonates could be removed by pumping at elevated temperatures, which was, however, not possible in the case of alkaline earth-exchanged zeolites. 

For both kinds of queries, methods for representation and manipulation of structures and spectra in databases are needed. In addition, problems of data exchange formats, for example, between a measured spectrum and a spectrum of a database, are to be decided. 

H atoms In the SD file exported by Beilstein structures are coded without H atoms. H atoms are, however, requited for calculating some indices and for calculating 3D molecular models. H atoms were thus added according to the valences of all non-H atoms. (The MDL SD file format is a popular exchange format for molecular structures, see [53]. 

Gasteiger, J. Hendriks, B.M.P. Hoever, P. Jochum, C. Somberg, H. JCAMP-CS. A Standard Exchange Format for Chemical Structure Information in Computer-Readable Form . Submitted for pubhcation in Appl. Spectrosc. 

Active species in the polymerization of cyclic acetals undergo fast isomerization. This results in chain transfer to polymer, that is, formation (by intramolecular reaction) of cyclic structures or formation (by intermolecular reaction) of branched oxonium ions, followed by exchange of the linear fragments of the chain (transacetaiization) (cf. Scheme 18). 

Chemical Abstracts Service Information System Electronic Laboratory Notebooks Internet Internet-based Computational Chemistry Tools Laboratory Information Management Systems (LIMS) Online Databases in Chemistry Spectroscopic Databases Standard Exchange Formats for Spectral Data Structure and Substructure Searching. 

ASN.l data description is especially relevant for distributed object systems and transparent multi-database access. The CXF chemical structure data exchange format of CAS is an example of a chemical ASN. 1 application. 

Circular Dichroism Electronic Computer Graphics and Molecular Modeling Electronic Laboratory Notebooks Electronic Publishing of Scientific Manuscripts Factual Information Databases Internet Molecular Models Visualization Object-oriented Programming Online Databases in Chemistry Standard Exchange Formats for Spectral Data Structural Similarity Measures for Database Searching. 

Computation Structural Applications Spectroscopic Databases Standard Exchange Formats for Spectral Data Structure Databases Structure Determination by Computer-based Spectrum Interpretation Structure Representation Topological Methods in Chemical Structure and Bonding, ... 

Chemical structure description has been done by following the JCAMP rules too. Today the MDL Information Systems, Inc. software, distributed worldwide, has defined a standard of its own. The Molfile and SDfile or RDfile formats serve as standards for structure exchange and are a more common alternative to the JCAMP format. 

Chemometrics Multivariate View on Chemical Problems Combinatorial Chemistry Factual Information Databases Fuzzy Methods in Chemistry Infrared Data Correlations with Chemical Structure Infrared Spectra Interpretation by the Characteristic Frequency Approach Inorganic Chemistry Databases Inorganic Compound Representation NMR Chemical Shift Computation Ab Initio NMR Chemical Shift Computation Structural Applications NMR Data Correlation with Chemical Structure Online Databases in Chemistry Spectroscopy Computational Methods Standard Exchange Formats for Spectral Data Structure and Substructure Searching Structure Determination by Computer-based Spectrum Interpretation Structure Generators Synthesis Design. 

This format has been developed to cover the core functionality of the first version of SMD using the syntactical structure of JCAMP-DX (see Standard Exchange Formats for Spectral... 

CXF (chemical exchange format) is CAS external structure and non-structural data format. The stereochemical features include (among others) CIP labels, template based labels, optical rotation, and coordination geometries with stereovertex lists. The format is designed to cover all details of CAS internal representation needed for the Registry service. ... 

Aspects of the development of exchange formats have been discussed by Baumgras and Rogers who have commented that at this time the Molfile offers the opportunity for a robust and complete means to transmit structures, but noted that the lack of standardization in the Molfiles created by [different programs] makes the Molfile unreliable for representation of many structures these views appear to be widely shared in the industry. 

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