Reactions, computer representation

Guthrie and Guthrie and Jencks have proposed an alternative mechanistic symbolism that is capable of more detailed description than the Ingold system, although at the expense of greater complexity. This system may be useful for the computer representation of reaction mechanisms. 

A methodology for computer representation of the structure of spatially complex multiphase media and for the modeling of reaction, transport, and structure-transformation processes in those media, is reviewed. 

For generating synthetic pathways by a computer, representations for the intermediates of chemical syntheses (molecules) and for the transformation intermediates of these (reactions) have to be designed. Both molecules and reactions are represented in our model of constitutional chemistry4 5 by matrices. Internally, in the program, more compact forms are used. 

The structures of chemical species have to be stored in a form which can be manipulated easily by the reaction generator that will predict the products of each elementary reaction. The computer representation must be unique and non-ambiguous so that reaction steps are not misinterpreted or repeated. As an example, for the neopentane + H atom reaction ... 

Based on user-defined simple bimolecular interactions the software package simmune generates computational representations of the complete set of multimolecular signaling complexes (up to a user-defined maximum size, i.e., number of molecular components) and their reactions. The software then allows its users to perform simulated experiments, exposing the simulated cells to stimuli either through the application of extracellular molecules or by letting the cells interact with other cells. Detailed information about the intracellular biochemistry of each simulated cell can be obtained and visualized in various ways. 

Bersohn M, Esack A (1977) A computer representation of synthetic organic reactions. Corn-put Chem 1(2) 103-107... 

Clearly, BE- and R-matrices have far too many entries of zero to be useful for direct computer implementation. Furthermore, the number of entries in BE- and R-matriccs incrcase.s by iV, N being the number of atoms in the molecule, so any implementation will try to use a representation such as a connection table where the mimbcr of entries increases linearly with the number of atoms. Using a connection table, an R-matrix will be stripped down to its non-zero elements. In the further discussion we will therefore only consider the bonds being broken and made in a reaction. 

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