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... 

The four Build Menus ia REACCS are Stmcture, Query, Top, and HighlightRxn. Stmcture menu contains the basic drawiag commands used to constmct the backbone of the stmcture. Query menu contains the commands used to add flexible stmctural parameters to the query. Top menu contains commands used to build reactions and to store and retrieve reactions, molecules, and graphic queries. HighlightRxn menu contains commands that apply atom/atom mapping and reaction centers to the current reaction. Atom/atom mapping is used to identify the reaction centers and iacrease accuracy and efficiency by letting the searcher specify that a particular atom ia a reactant must correspond to a particular atom ia the product. 

A synthesizer retrieves reactions according to functionality or substructure of the target molecule so fewer keys are needed than for a retriever program which requires entry by product reactants reaction type etc. Therefore file organization for one program is not necessarily optimal for the other. 

Recent developments are generic (Markush) structure storage and retrieval, reaction storage and retrieval, three-dimensional structure searches, and various extensions of documentation in molecular biology. 

It has been reported that a novel method for retrieving reactions similar to a given query reaction is to use relationships created by literature citations. Later publications citing a new reaction are likely to contain pertinent information about related reactions. In this study of all citing papers to 50 new s3oithetic methods indexed in Current Chemical Reactions, approximately half of the papers found by cited reference searching would not have been retrieved with reaction or substructure search approaches. 

The first commercial computer system to store, search and retrieve reaction schemes was ChemBase (see Figure 1). ChemBase could represent and display linear schemes, but was limited in its ability to perform scheme-oriented structure searches (see below). The Chemical Abstracts Service (CAS) has announced the availability of their reaction file (CASREACT)," organised with reaction schemes in mind. Although at present the scheme searching capabilities available at the user interface are limited, CASREACT appears to represent schemes in a more rigorous manner internally, allowing further user interface refinements in the future. 

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. 

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

Compounds are stored in reaction databases as connection tables (CT) in the same manner as in structure databases (see Section 5.11). Additionally, each compound is assigned information on the reaction center and the role of each compound in the specific reaction scheme (educt, product, etc.) (see Chapter 3). In addition to reaction data, the reaction database also includes bibliographic and factual information (solvent, yield, etc.). All these different data types render the integrated databases quite complex. The retrieval software must be able to recall all these different types of information. 

This tutorial describes briefly some of the search capabilities possible with Cheminform RX and MDL" ISIS used as the retrieval system. In this tutorial, the CIRX database. of the years 1992-1996 arc used, containing altogether 334 855 reactions. 

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. 

Figure 5-28. Reaction query for Example 2 "R indicates that the bond must be part of a ring system, and "53 represents an atom with three non-hydrogen attachments. The Chiral" flag is necessary to retrieve only molecules with the identical absolute stereoconfiguration.

One reaction is found after performing this search it is shown in Figure 5-29. Analysis of the reaction conditions by retrieving the catalyst/solvent and conditions 011117, reading the given literature for more information, solves the problem... 

The tutorial in Section 10.3.1.8 presents some of the various ways the information in the Biochemical Pathways database can be retrieved. In this tutorial the importance of searching for the reaction center, the atoms and bonds directly involved in the bond rearrangement scheme, is emphasized, It is a prerequisite for getting a deeper understanding of chemical reactions. 

The reaction database compiled on Biochemical Pathways can be accessed on the web and can be investigated with the retrieval system C ROL (Compound Access and Retrieval On Line) [211 that provides a variety of powerful search techniques. The Biochemical Pathways database is split into a database of chemical structures and a database of chemical reactions that can be searched independently but which have been provided with efficient crosslinks between these two databases. 

And last not least, we will have to see further improvements in the graphical user interfaces of software systems and the retrieval systems of databases in order to make software and databases more acceptable to the chemical community at large. Software and databases should speak the language a chemist is used to, with hand-drawn chemical structures and reaction equations, or even imderstand the spoken word - and only provide the desired information selectively, not buried in a phe of unnecessary output. 

With its flexible and logical search language, REACCS can retrieve molecular stmctures, the atoms and bonds that are transformed ia a reaction, relative and absolute stereochemistry, the role (reactant, product, solvent, or catalyst) of a molecule ia a reaction, reaction data (eg, temperature and yield), hterature references, and keyword descriptions of reaction types. 

A number of methods have been developed to introduce context to on-line databases, enabling searches to be refined to minimized false retrieval. One of the earliest techniques is proximity searching, in which two words are required to be adjacent, or within a limited distance from each other in text. The assignment of roles to chemical substances is a method of precoordinating concepts. A substance can be identified as a reactant, as a product, and in some systems in a number of additional roles. For example, by searching for documents in which formaldehyde is a product, documents in which it is a reactant, or in which it undergoes no reaction, are thus eliminated. 

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