Molecular strain energy minimizing

The first four terms of the function are commonly found in molecular mechanics strain energy functions, and they are modified Hooke s law functions. The last term has been added to insure the proper stereochemistry about asymmetric atoms. A model is refined by minimizing the highly nonlinear strain energy function with respect to the atomic coordinates. An adaptive pattern search routine is used for the strain energy minimization because it does not require analytical derivatives. The time necessary to obtain good molecular models depends on the number of atoms in the molecule, the flexibility of the structure, and the quality of the starting model. 

Fig. 10. The acyclic quasilinear conformer of lasalocid anion which predominates under high polarity conditions. This conformer has the lowest intrinsic molecular strain energy as calculated using a QCFF energy minimization program - . Solvent effects on the conformation were modeled using an empirical specific site approach ...

The distorted structure can be replaced by a more reasonable structure using an empir ical molecular mechanics calculation This calculation which is invoked m Spartan Build by clicking on Minimize, automatically finds the structure with the smallest strain energy (m this case a structure with realistic bond distances and a boat conformation for the SIX membered ring)... 

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