Monte carlo simulations and experiments of all-silica zeolite LTA assembly combining structure directing agents that match cage sizes.

We investigated the influence of organic structure-directing agents (OSDAs) on the formation rates of all-silica zeolite LTA using both simulations and experiments, to shed light on the crystallization process. We compared syntheses using one OSDA with a diameter close to the size of the large cavity in LTA, and two OSDAs of diameters matching the sizes of both the small and large LTA cavities. Reaction-ensemble Monte Carlo (RxMC) simulations predict a speed up of LTA formation using two OSDAs matching the LTA pore sizes; this qualitative result is confirmed by experimental studies of crystallization kinetics, which find a speedup in all-silica LTA crystallization of a factor of 3. Analyses of simulated rings and their Si-O-Si angular energies during RxMC crystallizations show that all ring sizes in the faster crystallization exhibit lower angular energies, on average, than in the slower crystallization, explaining the origin of the speedup through packing effects.

Effects of Model Shape, Volume, and Softness of the Capsid for DNA Packaging of phi29.

Double-stranded DNA is under extreme confinement when packed in phage phi29 with osmotic pressures approaching 60 atm and densities near liquid crystalline. The shape of the capsid determined from experiment is elongated. We consider the effects of the capsid shape and volume on the DNA distribution. We propose simple models for the capsid of phage phi29 to capture volume, shape, and wall flexibility, leading to an accurate DNA density profile. The effect of the packaging motor twisting the DNA on the resulting density distribution has been explored. We find packing motor induced twisting leads to a greater numbers of defects formed. The emergence of defects such as bubbles or large roll angles along the DNA shows a sequence dependence, and the resulting flexibility leads to an inhomogeneous distribution of defects occurring more often at TpA steps and AT-rich regions. In conjunction with capsid elongation, this has effects on the global DNA packing structures.

Structure and the role of filling rate on model dsDNA packed in a phage capsid.

The conformation of DNA inside bacteriophages is of paramount importance for understanding packaging and ejection mechanisms. Models describing the structure of the confined macromolecule have depicted highly ordered conformations, such as spooled or toroidal arrangements that focus on reproducing experimental results obtained by averaging over thousands of configurations. However, it has been seen that more disordered states, including DNA kinking and the presence of domains with different DNA orientation can also accurately reproduce many of the structural experiments. In this work we have compared the results obtained through different simulated filling rates. We find a rate dependence for the resulting constrained states showing different anisotropic configurations. We present a quantitative analysis of the density distribution and the DNA orientation across the capsid showing excellent agreement with structural experiments. Second, we have analyzed the correlations within the capsid, finding evidence of the presence of domains characterized by aligned segments of DNA characterized by the structure factor. Finally, we have measured the number and distribution of DNA defects such as the emergence of bubbles and kinks as function of the filling rate. We find the slower the rate the fewer kink defects that appear and they would be unlikely at experimental filling rates with our model parameters. DNA domains of various orientation get larger with slower rates.

Modeling the Role of Excluded Volume in Zeolite Structure Direction.

We investigate the formation of zeolite structures in replica-exchange Monte Carlo simulations of a reactive model of silica polymerization. The simulations incorporate hard spheres to model the effect of excluded volume caused by structure-directing agents (SDAs). We focus on modeling the formation of cage-type zeolite frameworks SOD and LTA. Our model predicts that a relatively wide range of SDA sizes could be used to construct SOD, whereas a narrower range will work for constructing LTA. We also predict that there is potential benefit of including multiple SDAs in each zeolite unit cell, and in the case of LTA with both small and large cavities, there is a strong potential benefit using both small and large SDAs that match the cavities' sizes. We hypothesize that the volume exclusion reduces the configuration space available to the assembling silica units, making it easier for the system to find ordered structures with quasi-spherical cavities.

An integral equation and simulation study of hydrogen inclusions in a molecular crystal of short-capped nanotubes.

In this work we have assessed the ability of a recently proposed three-dimensional integral equation approach to describe the explicit spatial distribution of molecular hydrogen confined in a crystal formed by short-capped nanotubes of C50 H10. To that aim we have resorted to extensive molecular simulation calculations whose results have been compared with our three-dimensional integral equation approximation. We have first tested the ability of a single C50 H10 nanocage for the encapsulation of H2 by means of molecular dynamics simulations, in particular using targeted molecular dynamics to estimate the binding Gibbs energy of a host hydrogen molecule inside the nanocage. Then, we have investigated the adsorption isotherm of the nanocage crystal using grand canonical Monte Carlo simulations in order to evaluate the maximum load of molecular hydrogen. For a packing close to the maximum load explicit hydrogen density maps and density profiles have been determined using molecular dynamics simulations and the three-dimensional Ornstein-Zernike equation with a hypernetted chain closure. In these conditions of extremely tight confinement the theoretical approach has shown to be able to reproduce the three-dimensional structure of the adsorbed fluid with accuracy down to the finest details.

A three dimensional integral equation approach for fluids under confinement: Argon in zeolites.

In this work, we explore the ability of an inhomogeneous integral equation approach to provide a full three dimensional description of simple fluids under conditions of confinement in porous media. Explicitly, we will consider the case of argon adsorbed into silicalite-1, silicalite-2, and an all-silica analogue of faujasite, with a porous structure composed of linear (and zig-zag in the case of silicalite-1) channels of 5-8 Å diameter. The equation is based on the three dimensional Ornstein-Zernike approximation proposed by Beglov and Roux [J. Chem. Phys. 103, 360 (1995)] in combination with the use of an approximate fluid-fluid direct correlation function furnished by the replica Ornstein-Zernike equation with a hypernetted chain closure. Comparison with the results of grand canonical Monte Carlo/molecular dynamics simulations evidences that the theory provides an accurate description for the three dimensional density distribution of the adsorbed fluid, both at the level of density profiles and bidimensional density maps across representative sections of the porous material. In the case of very tight confinement (silicalite-1 and silicalite-2), solutions at low temperatures could not be found due to convergence difficulties, but for faujasite, which presents substantially larger channels, temperatures as low as 77 K are accessible to the integral equation. The overall results indicate that the theoretical approximation can be an excellent tool to characterize the microscopic adsorption behavior of porous materials.

Pattern formation in binary fluid mixtures induced by short-range competing interactions.

Molecular dynamics simulations and integral equation calculations of a simple equimolar mixture of diatomic molecules and monomers interacting via attractive and repulsive short-range potentials show the existence of pattern formation (microheterogeneity), mostly due to depletion forces away from the demixing region. Effective site-site potentials extracted from the pair correlation functions using an inverse Monte Carlo approach and an integral equation inversion procedure exhibit the features characteristic of a short-range attractive and a long-range repulsive potential. When charges are incorporated into the model, this becomes a coarse grained representation of a room temperature ionic liquid, and as expected, intermediate range order becomes more pronounced and stable.

Inclusions of a two dimensional fluid with competing interactions in a disordered, porous matrix.

The behavior of a fluid with competing interaction ranges adsorbed in a controlled pore size disordered matrix is studied by means of grand canonical Monte Carlo simulations in order to analyze the effects of confinement. The disordered matrix model is constructed from a two-dimensional non-additive hard-sphere fluid (which shows close to its demixing critical point large fluctuations in the concentration), after a subsequent quenching of the particle positions and removal of one of the components. The topology of the porous network is analyzed by means of a Delaunay tessellation procedure. The porous cavities are large enough to allow for cluster formation, which is however somewhat hindered as a result of the confinement, as seen from the comparison of cluster size distributions calculated for the fluid under confinement and in the bulk. The occurrence of lamellar phases is impeded by the disordered nature of the porous network. Analysis of two-dimensional density maps of the adsorbed fluid for given matrix configurations shows that clusters tend to build up in specific locations of the porous matrix, so as to minimize inter-cluster repulsion.

Explicit spatial description of fluid inclusions in porous matrices in terms of an inhomogeneous integral equation.

We study the fluid inclusion of both Lennard-Jones (LJ) particles and particles with competing interaction ranges--short range attractive and long range repulsive (SALR)--in a disordered porous medium constructed as a controlled pore glass in two dimensions. With the aid of a full two-dimensional Ornstein-Zernike approach, complemented by a Replica Ornstein-Zernike integral equation, we explicitly obtain the spatial density distribution of the fluid adsorbed in the porous matrix and a good approximation for the average fluid-matrix correlations. The results illustrate the remarkable differences between the adsorbed LJ and SALR systems. In the latter instance, particles tend to aggregate in clusters which occupy pockets and bays in the porous structure, whereas the LJ fluid uniformly wets the porous walls. A comparison with Molecular Dynamics simulations shows that the two-dimensional Ornstein-Zernike approach with a Hypernetted Chain closure together with a sensible approximation for the fluid-fluid correlations can provide an accurate picture of the spatial distribution of adsorbed fluids for a given configuration of porous material.

Carbon Nanotube Container: Complexes of C50H10 with Small Molecules.

The stability of complexes of a recently synthetized (Scott et al. J. Am. Chem. Soc.2011, 134, 107) opened nanocontainer C50H10 with several guest molecules, H2, N2, CO, HCN, H2O, CO2, CS2, H2S, C2H2, NH3, CH4, CH3CN, CH3OH, CH3CCH, 2-butyne, methyl halides, and with noble gas atoms, has been examined by means of symmetry-adapted perturbation theory of intermolecular interactions, which fully incorporates all important energy components, including a difficult dispersion term. All complexes under scrutiny have been found stable for all studied guests at 0 K, but entropic effects cause many of them to dissociate into constituent molecules under standard conditions. The estimation of temperature at which the Gibbs free energy ΔG = 0 revealed that the recently observed (Scott et al. J. Am. Chem. Soc.2011, 134, 107) complex CS2@C50H10 is the most stable at room temperature while the corresponding complexes with HCN and Xe guests should decompose at ca. 310 K and that with CO2 at room temperature (ca. 300 K). In agreement with the ΔG estimation, molecular dynamics simulations performed in vacuum for the CS2@C50H10 complex predicted that the complex is stable but decomposes at ca. 350 K. The MD simulations in CHCl3 solution showed that the presence of solvent stabilizes the CS2@C50H10 complex in comparison to vacuum. Thus, for the complexes obtained in solution the CO2 gas responsible for the greenhouse effect could be stored in the C50H10 nanotube.