Cubic section model Jones

Figure 7. Diamond lattice and Jones cubic section model.

In 1982 Jones and Jacovac mechanically constructed a cubic section model using Framework Molecular Models." The cubic section model was conceived because... 

The goal of the present study was to develop a computer-based cubic section model of the substrate binding domain of HLADH. It was considered that the Jones cubic section model could be refined by use of computer assisted substrate overlay in combination with kinetic data on a wide variety of substrates. As in the Jones approach we used the alcohol products as the surrogate substrate structures. Thus, we determined the low energy conformation of alcohols produced from ketones that have been reported to be reduced by HLADH and for which comparative kinetic data vs cyclohexanol could be calculated. As well, we determined the preferred conformations of all alcohols that would have been produced from ketones subjected to but failing to undergo HLADH reduction. These calculations utilised molecular mechanics (MACROMODEL) and yielded accurate co-ordinates for ali atoms in each alcohol. Where enantiomeric or stereoisomeric alcohols were produced or capable of production, the co-ordinates of each were calculated. 

As in the Jones protocol the cubic section model of the substrate binding domain of HLADH were constructed using structures of alcohol products rather than ketone substrates. The alcohol products were originally chosen by the Jones group because the transition state the geometry for the reduction was considered to resemble that of the alcohol rather than that of the ketone. The relative rate of reduction of substrate vs cyclohexanone for each ketone was required to be known. Furthermore, configurations of alcohol products, enantiomeric excess values, yields and % conversion of substrate required for calculation of the priority number for each enantiomer of product should be measured under comparable conditions (i.e. pH, temperature, concentration of enzyme, coenzyme and substrate, etc.). According to Alderweireldt et al. (1988) HLADH models are valid only for reaction conditions used in the reactions from which the models are constructed. Furthermore, the model is oniy reliable if the reactions have been conducted under kinetic control. 

Structurally rigid substrate surrogates were added to the cubic section model before more flexible molecules as the following order signifies pentacyclic, tetracyclic, tricyclic, bicyclic ketones, trans/cis-decalones, methyl cyclohexanones and alkyl cyclohexanones. The hydroxyls of cyclohexanols were oriented axially with respect to cyclohexyl rings consistent with the Jones protocol and with the obsen/ation that... 

A goal of this work was to refine the cubic section model developed by Jones using computer modelling. Thus, equivalent orientations of compounds, cube size, I.SA. and origin location were used to construct the cubic section models of HLADH. Because the jacks and plastic tubing of the mechanical model occupy space, Jones changed... 

Figure 16. Cubic section modei for the substrate binding domain of HLADH Jones model (left) and the present (col3, right). Jones assigned each cube alphabetically and we have used his convention to allow comparison. The priority numbers for each cube were rounded in the present model.

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