Molecular simulation of RMM: ordered mesoporous SBA-15 type material having microporous ZSM-5 walls

SBA-15 is a novel porous material with uniform size mesopores arranged in a regular pattern. The adjacent mesopores are connected to each other by microporous walls. The major disadvantages of these materials are that the walls are amorphous and have low thermal, hydrothermal, and mechanical stability. Recently, there have been a few attempts to either coat the walls of SBA-15 by microporous crystalline zeolites or to fabricate SBA-15 using CMK-3 in such a way that the walls are made up of ZSM-5. The present work provides a first-ever study of RMM (replicated mesoporous materials, which are SBA-15 like ordered mesoporous materials with walls made up of ZSM-5) using molecular modeling. A random orientation of the unit cells and the distribution of sizes of the supercells located at nucleation sites would be ideal to model the RMM. However, such a study would introduce more uncertainties with regard to voids between the individual supercells, noncrystalline silica, and the location of active sites where the nucleation occurs. In a simpler model studied in the present work, the walls of SBA-15 were made up of regularly arranged ZSM-5 having the same orientation. The structure was characterized by estimating the nitrogen accessible area/volume by Connolly surfaces, small-angle and wide-angle X-ray diffraction patterns, methane adsorption, and ice as a probe to study the pore structure. It was found that RMMs have significantly higher methane adsorption capacity compared to SBA-15 and the majority of methane is adsorbed in the microporous walls of RMM. Further research in the field of RMM is needed to obtain the details of zeolitic wall structure.     

Heats of adsorption of CO2 on high-silicon zeolites ZSM-5 and silicalite

The heat of adsorption of C0₂on NaZSM-5 at zero occupancy is 50.0 kJ/mole. The differential heats have two linearly descending segments, corresponding to the formation of two types of adsorption complexes with one or two C0₂ molecules, on the average. The heat of adsorption on silicalite coincides with the heat of adsorption of CO₂ on the noncationic segment of the NaZSM-5 zeolite structure (28–29 kJ/mole). The adsorbate-adsorbate interaction forces are not evident on the zeolites up to 1.5 mmole/g occupancy. The isotherms for the adsorption of C0₂ on zeolite NaZSM-5 and silicalite at 303 K in the occupancy region of 0–1.5 and 0–0.5 mmole/g are completely described by VMOT equations.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 11, pp. 2636–2638, November, 1989.     

Molecular dynamics simulation of swollen membrane of perfluorinated ionomer

Molecular dynamics simulations of the swollen membrane of perfluorinated ionomer, which is composed of poly(tetrafluoroethylene) backbones and perfluosulfonic pendant side chains, have been undertaken to analyze the static and dynamic properties of the water and the side chain in the membrane. The calculations were carried out for four different water contents, 5, 10, 20 and 40 wt %, at 358.15 K and 0.1 MPa. The results are summarized as follows: (1) The sulfonic acid is the unique site to which water molecules can bind, and the other sites in the pendant side chain have no bound water even at high water concentration. (2) Sulfonic acids aggregate in the short range within 4.6-7.7 A despite the electrostatic repulsion between them. In such aggregates, a water molecule bridges two sulfonic acids. (3) Pendant side chains prefer to orient perpendicular to the hydrophilic/hydrophobic interface, and long-range correlation of side chain orientations is observed at 20 and 40 wt % water uptake membranes. (4) In a low water uptake membrane, the dynamics of water is substantially restricted due to strong attractive interactions with acidic sites. In contrast, at high water content, even the water locating near the sulfonic acid is relatively mobile. The short residence time of the bound water reveals that such water can frequently exchange position with relatively free water, which locates in the center of water cluster, in highly swollen membranes.     

Molecular simulation of adsorption and diffusion of chlorinated alkenes in ZSM-5 zeolites

In this work, adsorption and diffusion of trichloroethylene (TCE) and tetrachloroethylene (PCE) in ZSM-5-type zeolites were studied using molecular simulation methods. Grand canonical Monte Carlo technique was to calculate adsorption isotherms and heats of vaporization of TCE and PCE in zeolite. The results demonstrated that the Pnma-P2(1)2(1)2(1) symmetry transition of the zeolite framework has no significant effect on the TCE adsorption capacity of the silicalite, but it causes an increase of the PCE adsorption capacity. Simulations using a silicalite framework with Pnma symmetry showed that the adsorption capacity of the silicalite was limited to five molecules per unit cell. However, when a framework with P2(1)2(1)2(1) symmetry was used in the simulations, the capacity reached to eight molecules per unit cell, which is the actual adsorption capacity. To calculate intracrystalline diffusion coefficients of these compounds, molecular dynamics simulations were performed at different temperatures and loadings. The results show that the zeolite symmetry has a significant impact on diffusion coefficients of the sorbate molecules.     

Separation of acetic acid-water mixtures by pervaporation through silicalite membrane

Polycrystalline silicalite membranes were prepared on two kinds of porous supports by hydrothermal synthesis. The pervaporation performance of the silicalite membrane obtained was investigated using an acetic acid-water mixture as a feed. The silicalite membrane on the sintered stainless steel support selectively permeates acetic acid in the concentration of the feed acetic acid in the region of 5 to 40 vol%. However, the membrane on the porous alumina support showed no separation for the aqueous acetic acid solution. From the fact that the top layer of the membrane on the alumina support was not composed of pure silicalite but ZSM-5 zeolite crystals, which contained Brønsted acidic sites (Si(OH)Al) in the framework, it was suggested that the acidic sites associated with the framework aluminums play an important role in the separation of the acetic acid-water mixture. A long-term test of the pervaporation was also carried out to clarify the stability of the membrane.     

Molecular dynamics calculations of CO2/N2 mixture through the NaY type zeolite membrane

The separation of carbon dioxide from the carbon dioxide and nitrogen mixture, using NaY inorganic separation membrane, was calculated by molecular dynamics (MD) method. Computer graphic images reveal that carbon dioxide molecules are adsorbed on the sodium cation, located at site II. This site plays an important role in the separation of carbon dioxide.     

Molecular simulation study of adsorption and diffusion on silicalite for a benzene/CO2 mixture

The adsorption and diffusion of a binary mixture of supercritical CO2 and benzene on silicalite (MFI-type) have been studied through the grand canonical Monte Carlo and molecular dynamics (MD) simulations. The adsorption behavior of pure CO2 on silicalite was discussed in detail from the adsorption isotherms, adsorption sites, interaction energies, and isosteric heats of adsorption. For the mixture, the influences of temperature, pressure and composition on the adsorption isotherms have been examined. The adsorption site behavior of the mixture has been analyzed, and benzene molecules get adsorbed preferentially in the more spacious channel intersection positions. These simulation results suggest that SC-CO2 fluid can be used as an efficient desorbent of larger aromatics in the zeolite material. The diffusion characteristic for the benzene/CO2 mixture was studied on the basis of MD simulation. It was found that the large coadsorbed benzene molecule has a pronounced effect on the CO2 diffusion in the mixture, while the mobility of benzene molecules is very small due to geometrical restrictions.     

NMR and X-ray diffraction studies of the influence of adsorbed molecule nature on phase transitions in a ZSM-5 silicalite

Pulsed NMR and X-ray diffraction analysis are employed to study the influence of adsorbed toluene, p-xylene, acetone, and di(ethylene glycol) (DEG) molecules on phase transitions in a ZSM-5 silicalite. In the region of phase transitions, times T₁ and T₂ of longitudinal and transverse magnetic relaxation of apolar molecules adsorbed in silicalite micropores increase and decrease in a jumpwise manner, respectively, with a rise in the total content of the liquid. Such changes in T₁ and T₂ occur for hexane, decane, toluene, and p-xylene molecules. Qualitatively different concentration dependences of T₁ and T₂ are observed for polar acetone and DEG molecules, because these liquids do not cause a earrangement in the crystal lattice of silicalite; this is confirmed by the X-ray diffraction data.Translated from Kolloidnyi Zhurnal, Vol. 66, No. 6, 2004, pp. 802–806.Original Russian Text Copyright © 2004 by Pimenov, Skirda, Maksimenko, Morozov, Opanasyuk.     

Passive transport of C60 fullerenes through a lipid membrane: a molecular dynamics simulation study

To investigate the implications of the unique properties of fullerenes on their interaction with and passive transport into lipid membranes, atomistic molecular dynamics simulations of a C60 fullerene in a fully hydrated di-myristoyl-phoshatidylcholine lipid membrane have been carried out. In these simulations the free energy and the diffusivity of the fullerene were obtained as a function of its position within the membrane. These properties were utilized to calculate the permeability of fullerenes through the lipid membrane. Simulations reveal that the free energy decreases as the fullerene passes from the aqueous phase, through the head group layer and into the hydrophobic core of the membrane. This decrease in free energy is not due to hydrophobic interactions but rather to stronger van der Waals (dispersion) interactions between the fullerene and the membrane compared to those between the fullerene and (bulk) water. It was found that there is no free energy barrier for transport of a fullerene from the aqueous phase into the lipid core of the membrane. In combination with strong partitioning of the fullerenes into the lipidic core of the membrane, this "barrierless" penetration results in an astonishingly large permeability of fullerenes through the lipid membrane, greater than observed for any other known penetrant. When the strength of the dispersion interactions between the fullerene and its surroundings is reduced in the simulations, thereby emulating a nanometer sized hydrophobic particle, a large free energy barrier for penetration of the head group layer emerges, indicating that the large permeability of fullerenes through lipid membranes is a result of their unique interaction with their surrounding medium.     

Effect of structural analogy between ZSM-5 and silicalite catalysts on the oxidative methylation of toluene with methane

Summary With ZSM-5 and silicalite (both initial and BaO modified) the yield of styrene, the most desirable reaction product, was highly represented when BaO modified silicalite was used as catalyst for the reaction. The catalytic results fitted the basicity, surface area and structural crystallinity.     

Molecular dynamics simulation of nonsteroidal antiinflammatory drugs,naproxen and relafen,in a lipid bilayer membrane

Naproxen and relafen, as nonsteroidal antiinflammatory drugs, were simulated in neutral and charged forms and their effects on a lipid bilayer membrane were investigated by molecular dynamics simulation using Groningen machine for chemical simulations software (GROMACS). Simulation of 10 systems was performed, which included different dosages of the drug molecules, naproxen and Relafen, in charged and neutral forms, and a mixture of naproxen and Relafen in neutral forms. The effects of the mixture and the individual drugs' dosages on membrane properties, such as electrostatic potential, order parameter, diffusion coefficients, and hydrogen bond formation, were analyzed. Hydration of the drugs in the membrane system was investigated using radial distribution function analysis. Using fully hydrated dimyristoylphosphatidylcholine (DMPC) as a reference system, 128 lipid molecules and water molecules were simulated exclusively, and the same simulation technique was performed on 10 other systems, including drug mixtures and a DMPC membrane. Angular distributions of lipid chains of the membrane were calculated, and the effects of the drug insertion and chain orientation in the membrane were evaluated. © 2013 Wiley Periodicals, Inc.     

Molecular simulation of the adsorption of MTBE in silicalite, mordenite, and zeolite beta

The use of methyl tertiary butyl ether (MTBE) as a gasoline additive has resulted in serious environmental problems following spills and leaks, primarily due to MTBE's high solubility in water. Remediation technologies have involved air stripping, advanced oxidation, and sorption on granular activated carbons (GAC). Hydrophobic zeolites, such as silicalite, dealuminated Y, mordenite, and beta, have been of interest in recent studies for the removal of MTBE from water. Some of these materials have shown a better performance than GAC particularly in the microg/L range. We made Monte Carlo and molecular dynamics simulations of the adsorption of pure MTBE in silicalite, mordenite, and zeolite beta with different Na+ loadings at room temperature to reveal the factors affecting the adsorption process. The results show that although the three zeolites studied here have similar pore volumes, the pore structure of zeolite beta causes a significant difference on the predicted amount of MTBE adsorbed. It was found that the position of the Na+ cations has an important effect at lower pressures. Within the range of [Na+] studied, the amount of Na+ was not found to be critical on the adsorption capacity of any of the zeolites studied, except at very low pressures in silicalite and zeolite beta.     

Molecular dynamics simulation of a water/metal interface

First results of a molecular dynamics study of a water/metal interface, lasting 3.3 ps at an average temperature of 294 K, are reported. The basic periodic box contains 216 water molecules and a crystal slab of 550 platinum atoms with (100) surface planes. A combination of a Lennard-Jones potential between centers of mass and a Coulomb potential arising from dielectric interactions of the water charge distribution with the metal is employed for the water-wall interaction, the ST2 model for the water-water, and a nearest-neighbour harmonic potential for the platinum-platinum interactions. Considerable adsorption at the interface together with a drastic change of the water structure is observed.     

Molecular dynamics simulation of semirigid polymers

The chain rigidity of poly(p-hydroxybenzoate) was estimated through the theoretical evaluation of its persistence length (L_p). A non-Brownian molecular dynamics (MD) simulation of an isolated chain with 20 monomeric units was performed. The sampled conformational population was analyzed and the orientational correlation function between monomeric units along the chain was calculated. An algorithm based on the worm-like chain model was applied to evaluate the persistence length. The results were compared with those obtained from equilibrium models like the freely-rotating-chain and the rotational-matrix method with fluctuations. Equilibrium models give different results depending on the degree of accuracy used in describing the monomeric unit. The inclusion of thermal fluctuations is crucial to obtain realistic results. These coincide with those given by MD simulation when only nearest-neighbour orientational correlations are taken into account: inclusion of higher-order correlation terms leads to lower values of the persistence length. The origin of this discrepancy was investigated. The MD simulation results are characterized by an overrepresentation of conformations with a short end-to-end distance resulting from an anomalous energy concentration in the first bending mode of the chain. In analogy with previous simulation results from systems characterized by a week coupling amoung their degrees of freedom, failure in the energy equipartition is proposed as a likely explanation of the anomalous dynamical behaviour.     

液态水的分子动力学模拟

用分子动力学(MD)模拟方法在150~376K的温度范围内对液态水的微正则系统进行了研究。考察了液态水的结构及其性质。模拟采用了由从头算得出的柔性水-水相互作用势MCYL。对时间和空间的平均得出了液态中水分子几何构型及温度改变所引起的液态水结构变化。对径向分布函数gOH, gOO, gHH及配位数的分析表明, 在所考察的温度范围内, 每个水分子与相邻分子形成的氢键数为2~3, 水分子在参与的2个氢键中同时作为授受体。结合对振动谱的研究表明在低温时液态水形成的网络结构可能随温度的升高而形成小的簇结构。     

Molecular dynamics simulation of liquid trimethylphosphine

Structural and dynamical properties of liquid trimethylphosphine (TMP), (CH(3))(3)P, as a function of temperature is investigated by molecular dynamics (MD) simulations. The force field used in the MD simulations, which has been proposed from molecular mechanics and quantum chemistry calculations, is able to reproduce the experimental density of liquid TMP at room temperature. Equilibrium structure is investigated by the usual radial distribution function, g(r), and also in the reciprocal space by the static structure factor, S(k). On the basis of center of mass distances, liquid TMP behaves like a simple liquid of almost spherical particles, but orientational correlation due to dipole-dipole interactions is revealed at short-range distances. Single particle and collective dynamics are investigated by several time correlation functions. At high temperatures, diffusion and reorientation occur at the same time range as relaxation of the liquid structure. Decoupling of these dynamic properties starts below ca. 220 K, when rattling dynamics of a given TMP molecules due to the cage effect of neighbouring molecules becomes important.     

Molecular dynamics simulation study on stabilities and reactivities of NADH cytochrome B5 reductase

Binding free energies between coenzyme (FAD and NADH) and the apoenzyme of NADH-cytochrome b5 reductase (b5R) were estimated by applying the continuum Poisson-Boltzmann (PB) model to structures sampled from molecular dynamics simulations in explicit water molecules. Important residues for the enzymatic catalysis were clarified using a computational alanine scanning method. The binding free energies calculated by applying an alanine scanning method can successfully reproduce the trends of the measured steady-state enzymatic activities kcatNADH/KmNADH. Significant decreases in the binding free energy are expected when one of the four residues Arg91, Lys110, Ser127, and Thr181 is mutated into Ala. According to the results of the molecular dynamics simulation, Thr181 is considered to be one of the key residues that helps NADH to approach the isoalloxazine in FAD. Finally, we have constructed very simplified model systems and carried out density functional theory calculations using B3LYP/LANL2DZ//ROHF(or RHF)/LANL2DZ level of theory in order to elucidate a realistic and feasible mechanism of the hydride-ion transfer from NADH to FAD affected by HEME(Fe3+) as an electron acceptor. Our calculated results suggest that the electron and/or hydride-ion transfer reaction from NADH to FAD can be accelerated in the presence of HEME(Fe3+).