RESUMO
Computation based on molecular models is playing an increasingly important role in biology, biological chemistry, and biophysics. Since only a very limited number of properties of biomolecular systems is actually accessible to measurement by experimental means, computer simulation can complement experiment by providing not only averages, but also distributions and time series of any definable quantity, for example, conformational distributions or interactions between parts of systems. Present day biomolecular modeling is limited in its application by four main problems: 1) the force-field problem, 2) the search (sampling) problem, 3) the ensemble (sampling) problem, and 4) the experimental problem. These four problems are discussed and illustrated by practical examples. Perspectives are also outlined for pushing forward the limitations of biomolecular modeling.
Assuntos
Modelos Biológicos , Modelos Moleculares , Proteínas/química , Simulação por Computador , Conformação Proteica , Dobramento de ProteínaRESUMO
A new force field for the simulation of the adsorption of cycloalkanes in nanoporous silica affords a significant improvement over any previously employed force field. The simulated isotherms reproduce the most salient features in the experimental isotherms extremely well. The study of cyclo-pentane, -hexane, and -heptane adsorption in MFI-type silica indicates an inflection for cyclopentane but not for cyclohexane at intermediate pressure. If corroborated by experiments, such an inflection point would afford an excellent calibration point for further force field developments. At low pressures, mixture isotherms of cyclohexane and n-hexane show a temperature dependence on the selectivity in accordance with recent results by J. P. Fox and S. P. Bates, J. Phys. Chem., 2004, 108, 17136. This dependence is caused by a difference in temperature dependence of the Henry coefficient for both molecules. At high pressures entropy effects due to packing always favor the sorption of n-hexane. Furthermore, the influence of the flexibility of the zeolite framework on the adsorption of these rather bulky molecules is investigated. It is found that this influence of the flexibility on the adsorption of cyclohexane is as small as with n-alkanes.
