Systems and Refined Models

Force Fields and Properties of Ionic Liquids Having Dialkylimidazolium Cations 

We finish the discussion of force fields developed for imidazolium-based systems by describing the work of Voth and co-workers who simulated [C2mim][N03] first with traditional fixed-charge models and then with a model that included electronic polarizability. For the fixed-charge system, Del Popolo and Voth used a force field having the AMBER function form, with parameters for the cation and anion taken from existing sources. They 

Del Popolo and Voth computed dynamical properties at 400 K and observed very long overall rotational relaxation times, consistent with the slow dynamics observed by Margulis, Stern, and Berne as well as by Morrow and Maginn. They showed the clearest evidence up to that point that the dynamic motion of ionic liquids bears a resemblance to that of supercooled or glassy systems, an issue that will be described more fully later in this chapter. 

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It should be remembered, of course, that scaling behavior is informative of the relative time one system takes compared to another of different size, and says nothing about the absolute time required for the calculation. Thus, FMM methods scale linearly, but the initial overhead can be quite large, so that it requires a very large system before it outperforms PME for the same level of accuracy. Nevertheless, the availability of the FMM method renders conceivable the molecular modeling of extraordinarily large systems, and refinements of the method are likely to be forthcoming. 

In view of the above comments, error estimates are usually made on the basis of overall reproducibility of, and matching between independent experimental or theoretical results, rather than on the basis of the precision reachable with a particular measurement and refinement model. There are several approaches that allow us to gain quantitative information on experimental reproducibility and uncertainties. These include the pseudoatom interpretation of error free, theoretical data [56, 57, 70-72], comparative analysis of experimental data sets in terms of different constrained models [73], theory versus experimental comparison of results obtained for the same system [74-76], systematic studies on a series of related compounds [77], and the simultaneous analysis of data collected at different temperatures [66]. 

Molecular dynamics (MD), while computationally very expensive, is often used to relax structures, relieve local strain, and refine models of macro-molecular structures or complexes of these with ligands docked into the receptor site. Basically, MD consists of solving Newton s equations of motion for each atom in a system as a function of time and energy funaions describing interatomic forces. > While calculating the atomic trajeaories is slow, once calculated these can be stored and often played back in real time, thus creating a picture of the system as it evolves over time. 

Various finite element models are developed to assess the flexibility of the system and these models represent a progression on the refinement of the system, which is required in order to produce a measure for the significant effects of the flexibility. 

Jones TA. A graphics model building and refinement system for macromolecules. JAppl Cryst 1918 11 268. 

The reactor system works nicely and two model systems were studied in detail catalytic hydrogenation of citral to citronellal and citronellol on Ni (application in perfumery industty) and ring opening of decalin on supported Ir and Pt catalysts (application in oil refining to get better diesel oil). Both systems represent very complex parallel-consecutive reaction schemes. Various temperatures, catalyst particle sizes and flow rates were thoroughly screened. 

RCRA covers were constructed in 1995, and the ET covers were constructed in 1996. All of the covers are 43 ft wide by 328 ft long and were seeded with native vegetation. The purpose of the project is to use the performance data to help demonstrate equivalency and refine numerical models to more accurately predict cover system performance.39... 

One way to separate concerns at the business and requirements levels is according to the point of view of different categories of users—a particular kind of subject area. This approach gives you different models of the same types and actions (they must be combined at some stage before you can build a system). You base your views on the high-level actions of those users. Each action needs a model to specify what it achieves and needs additional static and dynamic models to refine it into finer-grained actions. 

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