Structure reaction file

A hierarchy is thereby achieved, that will lead to a reaction file structure, where each entry is referenced through the various levels of specificity up to the R-categories. Queries can be entered at any degree of generality. 

The Chemistry of Heterocyclic Compounds, has been published since 1950 under the initial editorship of Arnold Weissberger, and later, until his death in 1984, under the joint editorship of Arnold Weissberger and Edward C. Taylor. In 1997, Peter Wipf joined Prof. Taylor as editor. This series attempts to make the extraordinarily complex and diverse filed of heterocylic chemistry as organized and readily accessible as possible. Each volume has traditionally dealt with syntheses, reactions, properties, structure, physical chemistry, and utility of compounds belonging to a specific ring system or class (e.g., pyridines, thiophenes, pyrimidines, three-membered ring systems). This series has become the basic reference collection for information on heterocyclic compounds. 

These files serve several other functions. Each reaction stored in CHESS needs to know structures of products and reactants. This is accomplished using reference numbers that point to the molecular reaction files of CHESS. Other knowledge must be placed into these reaction libraries. All of the information must be represented in such a way as to permit CHESS to reason on the stored reaction mechanisms. 

One of the few examples of commercially available retrieval systems encompassing both compounds and reactions is Molecular Design s microcomputer-based ChemBase system. It saves molfiles (molecular structure files) separately from its reaction file without any elaborate linkages between the files. This makes it rather difficult to move information between the files and requires the conversion of a molfile to move it in or out of a reaction file. Additionally, searching a compound structure for where it appears in a reaction is not a simple operation. Lastly, reaction sites are neither identified nor searchable. These limitations could be overcome if the reaction site could be associated with the molfiles or reaction files stored for searching. 

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. 

Figure 2. The structure of a REACCS reaction file. It consists of two linked databases one for reactions, and one for molecules...

In order to create subsets of this large reaction file, which can be searched on-line via STN International or with commercial in-house retrieval systems such as REACCS/ISIS from MDL Information Systems, Inc. (USA), a sophisticated algorithm has been developed by InfoChem which identifies the different reaction types in this large database. This InfoChem Classification Algorithm is currently the only available concept for structuring large reaction databases and has, therefore, a high commercial value. 

The different internal and external file formats make it necessary to have programs which convert one format into another. One of the first conversion programs for chemical structure information was Babel (around 1992). It supports almost 50 data formats for input and output of chemical structure information [61]. CLIFF is another file format converter based on the CACTVS technology and which supports nearly the same number of file formats [29]. In contrast to Babel, the program is more comprehensive it is able to convert chemical reaction information, and can calculate missing atom coordinates [29]. 

A larger number of features are provided by the ACDStructure Drawing Applet (ACDLabs). Both structures and reactions can be drawn, imported, and also exported. This applet supports Molfiles and has a large, integrated collection of pre-defined templates, which are extensible by the user. Additionally, gif files can be exported. It is not possible to draw or to Lmport/export chemical reactions. 

Here is the input file for an optimization of the transition structure for the reaction H3CO —t H2COH (a simple 1,2 hydrogen shift reaction). We specify a UHF calculation (open shell) since the molecular system is a doublet ... 

Perform the IRC calculation (requested with the IRC keyword). This job will help you to verify that you have the correct transition state for the reaction when you examine the structures that are downhill from the saddle point. In some cases, however, you will need to increase the number of steps taken in the IRC in order to get closer to the minimum the AAoxPoinb option specifies the number of steps to take in each direction as its argument. You can also continue an IRC calculation by using the lRC=(ReStorhMaxPointe=n) keyword, setting n to some appropriate value (provided, of course, that you have saved the checkpoint file). 

The predicted metabolites are also the starting point for the phase II metabolic prediction, to find where glucuronidation could occur. All the probable metabolites obtained from CYP metabolism reactions are submitted to a possible phase II reaction catalyzed by UGTs, using the UGT structure(s) as a template. The accessibility component is computed in the UGTcavity to prioritize glucuronic acid transfer. The final metabolite structures are then reported in graphical output or saved to a file. 

On file other hand, this reaction is endothermic by almost 10 kJ mol-1 in file solid state. This is surprising because the monoamine has a nonzero dipole moment and a molecular structure that allows forformation of linear arrays of intermolecularly N H—C hydrogen-bonded molecules in the crystal, while file other species have zero dipoles and lack the possibility of such stabilization... 

The first task of chemoinformatics is to transform chemical knowledge, such as molecular structures and chemical reactions, into computer-legible digital information. The digital representations of chemical information are the foundation for all chemoin-formatic manipulations in computer. There are many file formats for molecular information to be imported into and exported from computer. Some formats contain more information than others. Usually, intended applications will dictate which format is more suitable. For example, in a quantum chemistry calculation the molecular input file usually includes atomic symbols with three-dimensional (3D) atomic coordinates as the atomic positions, while a molecular dynamics simulation needs, in addition, atom types, bond status, and other relevant information for defining a force field. 

One of the most widely used chemical structure-encoding schemas in the pharmaceutical industry is the MDL Connection Table (CT) File Format. Both Molfile and SD File are based on MDL CT File Format to represent chemical structures. A Molfile represents a single chemical structure. An SD File contains one to many records, each of which has a chemical structure and other data that are associated with the structure. MDL Connection Table File Format also supports RG File to describe a single Rgroup query, rxnfile, which contains structural information of a single reaction, RD File, which has one to many records, each of which has a reaction and data associated with the reaction, and lastly, MDL s newly developed XML representation of the above—XD File. The CT File Format definition can be downloaded from the MDL website http //www.mdl.com/downloads/public/ctfile/ctfile.jsp. 

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