Reaction retriever

This tutorial, which is based on the Beilstein update BS0202PR (May, 2002) and on the retrieval program Cro.ssFire Commander V6,. shows. some typical advanced search examples in the Beilstein database. It is assumed that the user already knows some of the basic features of the retrieval program. Moreover, in this tutorial the CrossFire Structure Editor is used instead of the (SIS/Draw Structure Editor. The first example is a combined application of structure aiM fact retrieval, whereas the second example demonstrates reaction retrieval. 

After return to the Commander window, the reaction retrieval may be executed separately 629 Dicls-Aldcr reactions between aliphatic dienes and cyclic dicno-pliiles are found. This partial result can be narrowed down by restricting tlie reaction conditions by means of the fact editor, The search field codes for the yield and the temperature can be found to be RX.NYD and RX.T, respectively, either by browsing the database structure or by applying the Find option, as described in the first example. To ensure that the retrieved reaction conditions belong to the same experiment, both search terms must be connected by means of the PROXIMITY operator. Before the retrieval is started, the option "Refine results in... 

Figure 5-23. Display of the first hit (in "Hit only format) of the reaction retrieval shown i Figure 5-22,...

In this section, the basic concepts of reaction retrieval are explained. The first example is concerned with finding an efficient way to reduce a 3-methy]cydohex-2-cnonc derivative to the corresponding 3-mcthylcyclohcx-2-cnol compound (see Figure 5-24). As this is a conventional organic reaction, the CIRX database should contain valuable information on how to syntbesi2e this product easily. 

First, a quei y must be drawn using the MOL" ISIS/Draw program. By using this reaction query, a eurrent reaction search " can be performed. This type of reaction retrieval compares the starting material and the product of the reaction query with all the reactions in the CIRX database. Both query structures must match exactly, including the implicit hydrogen atoms not shown in the reaction query. In this case, one hit is found in the CIRX databases. 

The next abstraction level of reaction retrieval is a so-called reaction substructure search in which both query structures arc considered as substructures. In the case of a reaction substructure search, no hydrogen atoms arc added internally during the execution of the search. Atoms which have their valencies not completely saturated are considered as open sites, where any hind ofelement could be bonded. 

The figures are annotated and little additional comment is required. Figure 4 illustrates retrieval of a structure and its supergraphs and subgraphs. Figure 5 illustrates reaction retrieval. 

All Basis Products in the PGVL have been explicitly enumerated to support numerous molecular design, fragment-based design, and 2D and 3D methods they also provide here a rigorous basis for the fuzzy reaction retrieval in the LEAP2 method. 

John Wiley, Science of Synthesis from Thieme Verlag, Comprehensive Asymmetric Catalysis - CAC from Springer) has been developed by InfoChem and allows the retrieval of structures, reactions and text. InfoChem s application global Major Reference Works (gMRW) makes the individual MRWs available in one application that enables global searches over the various MRW databases simultaneously. Currently scientist can perform structure, substructure, and reaction retrieval in approximately 250,000 reactions. 

J. B. Hendrickson and T. L. Snyder, WebReac-tions—Organic Reaction Retrieval System, available online at http //webreactions.net,ac-cessed on September 6,2002. 

Reaction Retrieval Systems - A classical application of computers in chemistry is information retrieval, and chemical reactions are amenable to this type of treatment.34 when a strategic plan for synthesis has been established, there is still a need for detailed consideration of reagents and reaction conditions - and a Theilheimer type system may be best for this purpose. Such a file of reactions is typically searched by type of starting material, type of product, type of reaction, or conditions. Such a system usually contains very specific reactions of... 

Ott, Martin A., Noordik, Jan H. 1992. "Computer Tools for Reaction Retrieval and Synthesis Planning in Organic Chemistry A Brief Review of Their History, Methods, and Programs." Recueil des travaux chimiques des Pays-Bas, lll(June) 239-246. 

Bawden, D. Wood, S.I. Design, Implementation and Evaluation of the CONTRAST Reaction Retrieval System. Chapter 7 in Modern Approaches to Chemical Reaction Searching Willett, P.Ed. Gower Aldershot, 1986. 

The second generation of reaction retrieval systems were more specifically tailored to the problem of efficient reaction retrieval, and specifically stored information relating to the atom-to-atom correspondences in going from reactants to products. Searches which made use of these correspondences were fast and essentially free from false drops. In addition these systems permitted extensive use of searches based on keywords or phrases, which are particularly useful when associated with a hierarchically structured thesaurus. 

Figure 2. Requirements for an Efficient Reaction Retrieval System.

A requirement of the integration shown in the scheme of Figure 1 is the capability for smooth data transfer. This is especially important in the area of reaction retrieval, particularly for the generation of special databases at mini/mainframe and microcomputer level and for the uploading and downloading of data. To ensure efficient transfer, data from various sources (e.g. REACCS, MACCS, ChemBase) should be compatible, the mechanism of transfer must be simple and fiexible (translation of data), and, most importantly, a standard format must be used. The standard for MDL software is the reaction datafile (RDfile, Figure 11), a further development of the standard SDfile for molecules. The RDfile contains complete structural information on reactants, products, catalysts, and solvents and all other pertinent data. 

The first task can be done very conveniently with the available reaction retrieval systems. The second task is either a synthesis retrieval or a S3mthesis proposal task. The reaction retrieval systems cannot yet handle the synthesis retrieval job, but the synthesis proposal task can be done with one of the synthesis planning programs. 

Interfacing between reaction retrieval and synthesis planning has so far been used for exchange of database information. But why go fiirther into an integrated system capable of query formulation and query translation ... 

Reaction retrieval deals with very precise full structure information but you have to be aware of different possible ways to define the reaction centres. Another problem is the various notations for certain functional groups (e.g., sulphur and phosphorus groups). The most restricting factor yet is the inability to search for reaction sequences. Because of this you have to guess how a one-pot reaction or a multistep sequence was stored in the database. As a consequence you miss the information (Figure 6). 

Integration of a synthesis planning system and a reaction retrieval system to explore individual steps for literature precedents would result in an extremely powerful design tool. 

Reaction retrieval system Synthesis planning system Spectral identification Molecular modelling system Interfaces to MM, QM and MD MD MD programs... 

Reaction retrieval systems are usually built without due connection with systems built earlier for the retrieval of compounds. This paper discusses options for a file organisation for a unified structural database of compounds and their reactions. Such a database has a potential for improved retrieval capabilities and high browsability. 

It is planned to produce an online version of the database, which will be implemented on STN International. For this purpose, a data file in standard format that can be used under Messenger software will be derived from the base file. (Stereochemical information will be kept in this file, even though Messenger cannot handle this information at present). The enhancements to Messenger developed at CAS for CASREACT, the online reaction retrieval system developed by CAS, will also be used for this database. The display capability of Messenger will, in this configuration, also allow for the display of the whole (multi-step) reaction schemes. 

On the other hand, the data in the base file may be converted into an SMD file (Standardised Molecular Data) which is used by the companies of the CASP pool in Europe for interchanging substance and reaction data. Interfaces to commercially available reaction retrieval systems, using the SMD data structure, exist or are being developed. In this way, in-house versions of the database to be used with REACCS, ORAC, SYNLIB, etc., will be made available. 

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