Effect of the cation model on the equilibrium structure of poly-L-glutamate in aqueous sodium chloride solution.

We demonstrate that different sets of Lennard-Jones parameters proposed for the Na(+) ion, in conjunction with the empirical combining rules routinely used in simulation packages, can lead to essentially different equilibrium structures for a deprotonated poly-L-glutamic acid molecule (poly-L-glutamate) dissolved in a 0.3M aqueous NaCl solution. It is, however, difficult to discriminate a priori between these model potentials; when investigating the structure of the Na(+)-solvation shell in bulk NaCl solution, all parameter sets lead to radial distribution functions and solvation numbers in broad agreement with the available experimental data. We do not find any such dependency of the equilibrium structure on the parameters associated with the Cl(-) ion. This work does not aim at recommending a particular set of parameters for any particular purpose. Instead, it stresses the model dependence of simulation results for complex systems such as biomolecules in solution and thus the difficulties if simulations are to be used for unbiased predictions, or to discriminate between contradictory experiments. However, this opens the possibility of validating a model specifically in view of analyzing experimental data believed to be reliable.

Water-Methanol Mixtures: Simulations of Mixing Properties over the Entire Range of Mole Fractions.

Numerous experimental and theoretical investigations have been devoted to the hydrogen bond in pure liquids and mixtures. Among the different theoretical approaches, molecular dynamics (MD) simulations are predominant in obtaining detailed information, on the molecular level, simultaneously on the structure and the dynamics. Water and methanol are the two most prominent hydrogen-bonded liquids, and they and their mixtures have consequently been the subject of many studies; we revisit here the problem of the mixtures. An important first step is to check whether a classical potential model, the components of which are deemed to be satisfactory for the pure liquids, is able to reproduce the known thermodynamic excess properties of the mixtures sufficiently well. We have used the available BJH (water) and PHH (methanol) flexible models because they are by construction mutually compatible and also well suited to study, in a second step, some dynamic property characteristic of hydrogen-bonded liquids. In this article we show that these models, after a slight reparametrization for use in NpT simulations, reproduce the essential features of the excess mixing and molar properties of water-methanol mixtures. Furthermore, in the pure liquids, the agreement of the radial distribution functions with experiment remains as satisfactory as before. Similarly, the translation self-diffusion coefficients D are modified by less than 10%. In the mixtures, they evolve nonmonotonously as a function of mole fraction.

Enantioselective recognition at mesoporous chiral metal surfaces.

Chirality is widespread in natural systems, and artificial reproduction of chiral recognition is a major scientific challenge, especially owing to various potential applications ranging from catalysis to sensing and separation science. In this context, molecular imprinting is a well-known approach for generating materials with enantioselective properties, and it has been successfully employed using polymers. However, it is particularly difficult to synthesize chiral metal matrices by this method. Here we report the fabrication of a chirally imprinted mesoporous metal, obtained by the electrochemical reduction of platinum salts in the presence of a liquid crystal phase and chiral template molecules. The porous platinum retains a chiral character after removal of the template molecules. A matrix obtained in this way exhibits a large active surface area due to its mesoporosity, and also shows a significant discrimination between two enantiomers, when they are probed using such materials as electrodes.

Different structures give similar vibrational spectra: the case of OH- in aqueous solution.

We have calculated the anharmonic OH(-)(aq) vibrational spectrum in aqueous solution with a "classical Monte Carlo simulation + QM/MM + vibrational" sequential approach. A new interaction model was used in the Monte Carlo simulations: a modified version of the charged-ring hydroxide-water model from the literature. This spectrum is compared with experiment and with a spectrum based on CPMD-generated structures, and the hydration structures and H-bonding for the two models are compared. We find that: (i) the solvent-induced frequency shift as well as the absolute OH(-) frequency are in good agreement with experiment using the two models; (ii) the Raman and IR bands are very similar, in agreement with experiment; (iii) the hydration structure and H-bonding around the ion are very different with the two ion-water interaction models (charged-ring and CPMD); (iv) a cancellation effect between different regions of the hydration shell makes the total spectra similar for the two interaction models, although their hydration structures are different; (v) the net OH(-) frequency shift is a blueshift of about +80 cm(-1) with respect to frequency of the gas-phase ion.

The permeation of methane molecules through silicalite-1 surfaces.

The permeation of methane molecules through the silicalite-1 surfaces with and without silanol groups has been studied by nonequilibrium molecular dynamics computer simulations. A newly fitted intermolecular potential between the methane molecules and the silanol is used. A control volume provides a nearly stationary gas phase close to the membrane. The nonequilibrium process of filling the (initially empty) membrane with methane molecules until saturation is considered, and the surface permeability has been evaluated. It turns out to be strongly influenced by the presence of silanol groups. Additionally it was found that for a large part of the loading process the particle stream into the zeolite membrane was nearly independent upon the deviation from equilibrium. This means that far from equilibrium the decay of this deviation does not follow an exponential law.

Structure and dynamics of water confined in single-wall nanotubes.

The structure and dynamics of water confined in model single-wall carbon- and boron-nitride nanotubes (called SWCNT and SWBNNT, respectively) of different diameters have been investigated by molecular dynamics (MD) simulations at room temperature. The simulations were performed on periodically extended nanotubes filled with an amount of water that was determined by soaking a section of the nanotube in a water box in an NpT simulation (1 atm, 298 K). All MD production simulations were performed in the canonical (NVT) ensemble at a temperature of 298 K. Water was described by the extended simple point charge (SPC/E) model. The wall-water interactions were varied, within reasonable limits, to study the effect of a modified hydrophobicity of the pore walls. We report distribution functions for the water in the tubes in spherical and cylindrical coordinates and then look at the single-molecule dynamics, in particular self-diffusion. While this motion is slowed down in narrow tubes, in keeping with previous findings (Liu et al. J. Chem. Phys. 2005, 123, 234701-234707; Liu and Wang. Phys. Rev. 2005, 72, 085420/1-085420/4; Liu et al. Langmuir 2005, 21, 12025-12030) bulk-water like self-diffusion coefficients are found in wider tubes, more or less independently of the wall-water interaction. There may, however, be an anomaly in the self-diffusion for the SWBNNT.