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.

Computer simulations of the adsorption of hydrocarbons in zeolites are usually performed using rigid zeolite frameworks. This allows for the use of grid interpolation techniques to compute the hydrocarbon-zeolite interaction very efficiently. In this paper, we investigate the influence of the framework flexibility on the adsorption properties of hydrocarbons adsorbed in the zeolite silicalite. We find that at low loading, the influence of the framework flexibility on the heat of adsorption and the Henry coefficient is quite small. However, for molecules such as isobutane and heptane with inflection behavior, the influence at high loading seems to be much larger.

Based on a comparison between simulated and measured adsorption properties, we demonstrate that both normal and monomethylparaffins are able to fully enter the pores of TON-, MTT-, and AEL-type molecular sieves. This disproves the theory that monomethylparaffins only partially enter these pores and that normal paraffins are predominantly hydroisomerized at the pore mouths of these sieves. Instead, we attribute the high selectivity for paraffins with terminal methyl groups to product shape selectivity, and the low selectivity for paraffins with neighboring methyl groups to transition state selectivity. These traditional shape selectivity concepts explain not only the detailed product distribution of n-heptane hydroconversion, but also that of longer-chain n-paraffins.

The adsorption and separation of linear ͑C 1 -nC 5 ͒ and branched ͑C 5 isomers͒ alkanes on single-walled carbon nanotube bundles at 300 K have been studied using configurational-bias Monte Carlo simulation. For pure linear alkanes, the limiting adsorption properties at zero coverage exhibit a linear relation with the alkane carbon number; the long alkane is more adsorbed at low pressures, but the reverse is found for the short alkane at high pressures. For pure branched alkanes, the linear isomer adsorbs to a greater extent than its branched counterpart. For a five-component mixture of C 1 -nC 5 linear alkanes, the long alkane adsorption first increases and then decreases with increasing pressure, but the short alkane adsorption continues increasing and progressively replaces the long alkane at high pressures due to the size entropy effect. All the linear alkanes adsorb into the internal annular sites with preferred alignment parallel to the nanotube axis on a bundle with a gap of 3.2 Å, and also intercalate the interstitial channels in a bundle with a gap of 4.2 Å. For a three-component mixture of C 5 isomers, the adsorption of each isomer increases with increasing pressure until saturation, though nC 5 increases more rapidly with pressure and is preferentially adsorbed due to the configurational entropy effect. All the C 5 isomers adsorb into the internal annular sites on a bundle with a gap of 3.2 Å, but only nC 5 also intercalates the interstitial channels on a bundle with a gap of 4.2 Å. This work suggests the possibility of separating alkane mixtures based on differences in either size or configuration, as a consequence of competitive adsorption on the carbon nanotube bundles.

We discuss and develop an entropy-driven principle for separating isomers of alkanes in the five to seven carbon atom range by adsorption on silicalite-1. The normal alkanes are preferentially adsorbed because of configurational entropy effects; they "pack" more efficiently within the channel structures of silicalite. To demonstrate the separation principle we carried out CBMC simulations to determine the isotherms of various mixtures of linear and branched alkanes in silicalite-1. We show that the configurational entropy effects manifest at loadings greater than 4 molecules/unit cell and the sorption favors the linear alkanes while the branched alkanes are virtually excluded from the silicalite matrix. Validation of the entropybased separation principle is obtained by analyzing the silicalite membrane permeation data published in the literature.