AMBER model compound calculations

The complete set of new parameters for the phosphate and phosphorothioate model compounds is given in Table II. The new atom type (SD) and parameters have been added to the AMBER 4.1 force field database for simulating proteins and nucleic acids. For completeness, we have also included a comparison of geometrical parameters taken from optimized model compound structures using the updated AMBER 4.1 force field and HF/6-31G basis set calculations. These values are given in Table III. 

Force fields for [BMIM][PF6] that explicitly treat aU hydrogens (all-atom models) were developed soon after this by Margulis et al. [14], and Morrow and Maginn [11], while Stassen and coworkers [83] published a force field for the [EMIM]+ and [BMIM]+ cations paired with tetrachloroaluminate and tetrafluoroborate anions. The force fields aU have similar functional forms, and parameters were again maiiily developed using literature force field parameters for similar compounds and ab initio calculations of single ions or ion pairs. In these and later studies, repulsion-dispersion parameters were generally adapted from those available from one of three popular force field databases (Amber [114], OPLS [118] and CHARMM [119]). For [BMIM][PF6], the added realism of the all-atom model enabled densities to be predicted vyithin 1% of the experimental value [11]. The first indications of restricted dynamics in these systems were also observed [11,14,15]. 

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