Reaction databases availability

Unfortunately, in most cases not all the available information on a reaction is given in the reaction equation in a publication, and even less so in reaction databases. To obtain a fuller picture of the reaction that was performed, the text describing the experimental procedure in the publication or a lab journal) would have to be consulted. Reaction products that are considered as trivial, such as water, alcohol, ammonia, nitrogen, etc., are generally not included in the reaction equation or mentioned in the text describing the experimental work. This poses serious problems for the automatic identification of the reaction center. It is highly desirable to have the full stoichiometry of a reaction specified in the equation. 

J.T. Bohlen, Chemlnform Electronic Journal and Chemlnform RX Reaction Database, New Developments in Software, Entwicklung in der Chemie, Vol. 10, Gesellschaft Deutscher Chenuker, Frankfurt, 1996, pp. 27-32 available... 

With the advent of reaction databases chemists now have a treasure trove of information on chemical reactions available at their fingertips (sec Sections 5,4, 5.6, 5.10, and 5.12 of this Textbook, and Chapter X, Section 3.1 oFthe Handbook), Thus, searches in reaction databases might provide an answer to a chemist s question on the product of a specilic reaction. 

Before concluding this section it should be emphasi/cd that knowledge extraction from reaction databases is still a challenging problem having many important applications. There is still room for new approaches to this task, Furthermore, groat efforts should be made to improve the depth of information stored in reaction databases. With the introduction of electronic lab journals, the primary information on a chemical reaction gained in the laboratoiy becomes directly available. 

The foUowing tables outline the bibhographic, business, stmcture, numeric, spectra, and reaction databases currentiy available their producers and vendors and the subject matter they cover. 

In this chapter, we discuss double layer theory and how it can be incorporated into a geochemical model. We will consider hydrous ferric oxide (FeOOH //IFO), which is one of the most important sorbing minerals at low temperature under oxidizing conditions. Sorption by hydrous ferric oxide has been widely studied and Dzombak and Morel (1990) have compiled an internally consistent database of its complexation reactions. The model we develop, however, is general and can be applied equally well to surface complexation with other metal oxides for which a reaction database is available. 

Chemical information is reported and recorded in many forms, and a wide vnriety of databases have evolved to collect the various types of informalion. Bibliographic, business, structure, numeric, spectra, and reaction databases currently arc available. 

Reactions. CASREACr File is a chemical reaction database containing over 118.500 records with rcacliun informalion derived from documents covered in the Organic Section of Chemical Abstracts. The tile is available from STN. 

However, the most common sources of different results are both based on the approach used for the calculation of the activity coefficient (chapter 1.1.2.6) and the thermodynamic data sets themselves (chapter 2.1.4), which provide the respective program with the fundamental geochemical information of each single species. The thermodynamic databases available partly use severely differing data with different solubility products, different species, minerals and reaction equations. Nordstrom et al (1979, 1990), Nordstrom Munoz (1994), Nordstrom (1996, 2004) discuss this inconsistency of thermodynamic datasets in detail. For some species, for which stability constants have been published, not even the existence of the respective species has been proved doubtless, as can been shown in the following example. 

Over the past 10-20 years the kinetic data base for reaction of OH radicals with atmospheric pollutants has improved dramatically to a point where uncertainties in koH are typically in the range 10-20%. Critically evaluated data for OH radical reactions of atmospheric importance are available in several excellent reviews [8,15,22,24,25]. Likewise there are also extensive databases available for NO3 [8,13] and O3 reactions [8]. 

The laboratory study of IS ion chemistry has its origins in measurements of bimolecular ion/molecule reaction kinetics. Experimental conditions that are found in most of the mass spectrometers employed in the measurement of bimolecular ion/molecule reactions are far from those found in the cold low-pressure environments of space. Nevertheless, because of the pressure independence of bimolecular reactions and the absence of significant activation energies in most bimolecular ion/molecule reactions, MS measurements performed here on earth do have relevance for the chemistry in space. The substantial database available in the early 1990s on the kinetics of bimolecular ion/molecule reactions important in IS chemistry [8-10] was obtained almost entirely using ion cyclotron resonance (ICR) and flow-tube (FT) mass spectrometry techniques. Both techniques are well established and continue to be used extensively for ion/ molecule reaction measurements generally. 

The appearance of the o-" parameter in a large number of reactions and interactions involving X-phenols indicates that the phenoxy radical can be a potent, reactive intermediate in myriad reactions. The availability of a fast, easily retrievable computerized database to corroborate this phenomenon was useful. This approach of lateral validation was crucial in establishing a QSAR model that was not only statistically significant but also mechanistically interpretable. 

Other relational structure/reaction database systems are available commercially. These include the Thor system from Daylight... 

Like CA, Beilstein is available on-line, with the useful search engine Crossfire Beilstein. The Beilstein database is one of the best databases for organic chemistry, particularly synthetic organic chemistry. It contains information on 9.4 million organic substances that have been fully characterized, as well as 9.8 million reactions. Information available includes ... 

Mention has already been made of the publications of Kerr and Moss [23] as a source of bibliography. The same works list information on the kinetics of the reactions surveyed. Although the information is not critically evaluated and is now slightly dated, the coverage is broad, and where no evaluation of data on a particular reaction is available, the Kerr and Moss collection provides a valuable source for the existing data as does the NIST database [22], also discussed in Section 3.3. This too lists the kinetics data and also provides a graphical presentation. 

The active development, support, and distribution of WODCA was stopped in 2005. The distributor. Molecular Networks — a spin-off of Gasteiger s research team — is currently developing a Web-based expert system called Retrosynthesis Browser (RSB) for retrosynthetic analysis of a given target compound. RSB scans reaction databases to suggest new synthetic routes and simultaneously searches in catalogs of available starting materials for the proposed precursors. 

At the time of this writing, the public databases available from Molecular Design, and their numbers of reactions are ... 

The main goal for the software system under development is to make available in machine-readable form all the information contained in Cheminform. In this way different kinds of indexes may be produced as well as data deaUng with selected parts of chemistry for specialised information services, either printed or on computer-readable media. But the most important fact is that the information in Cheminform contains all the data needed for a reaction database. 

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