Developing a Force Field

The bleomycins (Fig. 12.6) are a family of glycopeptide-derived antibiotics which are used in the treatment of various tumors. They bind iron in the blood and form an active hypervalent oxo-iron species. The two-dimensional structure is well known but no crystal structures of bleomycin or its metal complexes have been reported. The MM2 force field was modified and extended by modeling of the crystal structures of the cobalt complexes of two bleomycin analogues in order to develop a force field for... 

Force Field Parameters I Developing a Force Field for Cobalt(III)... 

As a general rule, the best approach when developing a force field for a metal complex is to use, without modification, the nonbonded interaction terms developed for organic compounds. The best known and most popular is the MM2 force field and this has been extended and adapted for modeling metal complexes by a number of groups1113 1161. Force fields developed for organic molecules do not have parameters for some of the elements present in metal complexes but reasonable estimates are available for most of theset57 59,65 96 120 123 13... 

De Vos Burchart et al. have recently developed a force field for modeling zeolites.21 The model originally was intended for all-silica zeolites but was quickly extended to aluminum-containing zeolites. The parameters were derived from several sources. Standard bond dissociation energies were used, and the force constants were refined to fit the structure of ZSM-5, the structure and frequencies of a-quartz, in addition to unit cell dimensions of other zeolites. With the all-silica model, the authors were able to calculate heats of formation... 

Vibrational spectra Develop a force field to explicitly distinguish between Al and Si in FAU-type zeolites 79 ... 

Based on DFT calculations on chlorophylls and, additionally, on ubiquinone and the RC main detergent, lauryl dimethylamine oxide or LDAO, we have then developed a force field for their classical modelization. Our approach to this undertaking was straightforward. We initially use the DFT optimized structures and the vibrational analysis to determine the bonded part of the potential parameters described by the AMBER potential function. Then, atomic ab initio partial charges on the chromophore are used to account for electrostatic effects. At a later stage, experimental data from X-ray crystallography are used to check the structural properties of the molecule in the condensed state and to refine the intermolecular Lennard-Jones parameters. 

One important point that we should bear in mind as we undertake a deeper analysis of molecular mechanics is that force fields are empirical-, there is no correct form for a force field. Of course, if one functional form is shown to perform better than another it is likely that form will be favoured. Most of the force fields in common use do have a very similar fqrm, and it is tempting to assume that this must therefore be the optimal functional form Certainly such models tend to conform to a useful picture of the interactions present in a system, but it should always be borne in mind that there may be better forms, particularly when developing a force field for new classes of molecule. The functional forms employed in molecular mechanics force fields are often a compromise between accuracy and computational efficiency the most accurate functional form may often be unsatisfactory for efficient computation. As the performance of computers increases so it becomes pcKsible to incorporate more sophisticated models. An additional consideration is that in order to use techniques such as energy minimisation and molecular dynamics, it is usually desirable to be able to calculate the first and second derivatives of the energy with respect to the atomic coordinates. 

---