Special reaction databases

Once the structure to be made has been identified, what is the most desirable route and which particular conditions are best for the individual steps (see Reaction Databases, Section 5.3.7) and what special reagents can be used (see Speciality reaction databases. Section 5.3.7.1) ... 

Whereas in Section II we assumed that the participating steps will be given for a particular application, here it is useful to have a database with the most common enzymatic reactions and compounds, so that one only needs to add the specialized reactions for a given investigation. 

Profile The company provides scientific information products and services to the fine-chemical, pharmaceutical, agrochemical, biotechnology, and academic research communities. Synopsys operates worldwide, with offices and distributors in Europe, the United States, and Japan. It specializes in chemical reaction databases that deliver added-value information and refined data. 

Common practice in indexing documents that discuss chemical reactions is to index each reaction in its own link. When role indicators are added, this technique simulates a reaction database. Roles are used for every chemical, but experience has shown that an elaborate set of roles leads to redundant indexing . This database uses reactant, product, special agent, medium, and other (used when the aforementioned do not apply). A typical record is illustrated by Figure 8. 

An explicit reaction scheme is one that has been reported in the literature. Explicit schemes may or may not be indexed in a special way in the reaction database system. Approximately 15% of the reactions in Theilheimer s Synthetic Methods are reported as reaction schemes. In the ORAC Theilheimer database, each individual reaction step and the overall transformation is stored as a separate entry. For example, a sequence A—>C— D is indexed as the three reactions A->B, B->C and C D, plus the overall transformation A- D. A drawback of this approach is that transformations such as B D cannot be located in answering a... 

CrossFire is the enhanced inhouse version of the Beilstein database. The database consists of about 30 million reports, of which five million are reactions. Hence this database is a reaction database. But apart from that, it covers structural, factual and bibliographic information. This means that CrossFire can also be classified as a structural and most of all as a numeric database. In a recently published article by Lawson, an example is shown, illustrating the use of substance-, reaction-, and document-based search techniques on the same problem. The special power of hyperlinks between reactions, substances, and documents is shown. 

SYNLIB is a very special reaction retrieval system, which differs significantly from other systems in terms of the underlying philosophy and functionality. It has a built-in fuzziness, such that usually not the entire (sub)structures entered are matched in the database, but only those parts of the query that the user declared as target (Figure 10). Target centers are usually reaction centers plus some parts of the environment . " ... 

The in-house systems REACCS, ISIS, and CrossFire handle aromaticity and tautomerism satisfactorily a user can enter structures as any chemist normally would without having to worry about the bond conventions used internally by the database system. This is not yet true for CASREACT and other reaction databases offered under STN Messenger. Here the user has to know the definition and use of normalized bonds, a special bond type defined to handle aromaticity and tautomerism in a formal way. This, unfortunately, corresponds only partially to these concepts ias used by chemists. CAS is working on Ais problem the SciFinder interface already offers a solution for exact structures, but not yet for substructures, falling into this category (see Structure Representation). 

Secondly, chemical IR may be thought of as a specialized index into the scientific and patent literature, with the chemical structure representing an extremely condensed abstract of the journal article or patent document. In this sense, the structures are not stored for their intrinsic interest, but as pointers to other documents, some of which, for example, may be related to their synthesis, physicochemical properties and numeric data, or applications. This is the sense in which a few data vendors supply chemical and reaction databases (Derwent and Institute for Scientific Information), and the alternate sense in which the CAS databases may be used. The use of CIR systems in synthesis design - providing access, for example, to databases of reagents or starting materials, or of name reactions - provides a crucial tool for the contemporary chemical and pharmaceutical industry. 

Other related coding languages are derived from enhancements of SMILES (XSMILES, SMARTS, SMIRKS, STRAPS, CHUCKLES, CHORTLES, CHARTS [22]). Each of them was designed to represent special molecular structures or to allow particular applications (polymers, mixtures, reactions, or database-handling). 

The Special Nutritionals Adverse Event Monitoring System (SN/AEMS) of the U.S. Food and Drug Administration (FDA), a database of consumer reactions to nutritional supplements and substances, has had 31 reports of adverse reactions to products containing creatine between 1993-1998. Reported symptoms include (but were not limited to) ... 

In the simplest sense, searching chemical information consists of (IXinding structures or reactions that meet the chemist s search criteria and/or (2) finding data that meets the search criteria. Data searching (numbers and text) is a well-established informatics activity, supported by spreadsheets, word processors, and relational database systems. Chemical structures and reactions are a unique form of data. Searching for full or partial matches to structures, models, and reactions requires highly specialized databases and search techniques. 

The construction of a fully automated laboratory where all manual steps - from chemical synthesis to product characterization - are managed by robots is no longer a futuristic dream. Currently, about 20 companies are specialized in the design of chemistry robots of different sizes and levels of automation [15,16 Chapt. 19]. The robotized laboratory for chemical synthesis has to be connected with databases for building blocks, for reaction information, and for library information.The tools for data analysis should be accessible to the operator to design libraries and lead optimization in cooperation with specialists for screening, bioinformatics, database management, computational and medicinal chemistry, and for compound characterization. 

As mentioned in Sect. 5.3.3, a number of enzymes contain metal ions that participate in the catalytic reaction. Two specialized databases store information on metal ions and other bioinorganic motifs in enzymes. PROMISE (prosthetic centers and metal ions in protein active sites) is maintained by the University of Leeds and focuses on six major groups of metal containing proteins diiron-carboxylate proteins, haem proteins, iron-sulfur proteins, molybdopterin proteins, mononuclear iron proteins, and chlorophyll containing proteins156. ... 

For batch, plug flow, and CSTR. Includes gas-phase isothermal, nonisothermal, and nonisobaric reactions, heterogeneous catalysis, and thermochemical database for calculation of equilibrium constants. Many subprograms for special situations (shock waves, flames, partially stirred reactors, etc.) are available. 

---