Automated Model Building

The mechanistic paraffin hydrocracking model builder has a database of all reaction matrices and rules for all mechanistic paraffin hydrocracking reactions, involving both metal and acid chemistries, with the flexibility of changing them. A detailed library of parafifins, olefins, and ion intermediates consisting of their connectivity and thermod5mamic information was built 

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For a detailed comparison of some popular automated model building packages, see Badger (2003). For an analysis of structural features and their relationship to model building strategies, see Morris (2004). Further details should be sought in the original articles. 

High resolution (between 1.4 and 2.0 A) Automated model building with ARP/wARP should work with most phase sets. RESOLVE, which uses a template-based rather than atom-based approach, should also perform well but may be computationally more consuming. Refinement can best be carried out with REEMAC or PHENIX using isotropic ADPs since the amount of data is no longer sufficient for an anisotropic description of atomic displacement parameters. The use of TLS (Winn et ah, 2003) is highly recommended. A use of NCS restraints should be critically evaluated and in most cases the refinement can proceed without them. Double conformations of side chains should be visible and modelled. Ordered solvent can be modelled automatically. 

Badger, J. (2003). An evaluation of automated model building procedures for protein crystallography. Acta Crystulhgr. D 59, 823-827. 

This section first discusses the reaction mechanism for paraffin hydrocracking and the thus-derived modeling specifications for each reaction family. This is followed by a discussion of the automated model building algorithm and the QSRC/LFERs used to organize the rate parameters. Finally, the thus-developed Cig paraffin mechanistic hydrocracking model diagnostics are presented. 

The reaction matrices of Table 1, the reaction rules of Table 2, the QSRC/LFER correlations of Eq. 1, and the automated model-building algorithm of Figure 3 were used to construct various kinetic model versions for mixtures containing molecules from C% to 24-... 

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