Prediction of adsorption of xenon in zeolite NaA with molecular density functional theory

The Tarazona model of molecular density functional theory is used to determine the adsorption isotherm and the density distribution of xenon atoms in zeolite NaA. We consider the alpha cage of NaA to be fully three-dimensional and we introduce a basis set for the density distribution to make the solution computationally tractable. The results of this density functional theory model are compared to previous results of grand canonical Monte Carlo simulations for the same system.We dedicate this paper to Professor Herbert Wagner, whose excellent contributions to density functional theory typify his valuable role in the advancement of statistical physics     

Diffusion of gases across lipid membranes with OmpA channel: a molecular dynamics study

Molecular transport across biological membranes occurs in a range of important chemical and biological processes. The biological membrane can usually be modelled as a phospholipid bilayer, but to correctly represent biological transport, the embedded transmembrane proteins must also be included. In previous molecular simulation studies on transport of small gas molecules in dipalmitoylphosphatidylcholine (DPPC) bilayer membrane, a coarse-grained model was used to provide direct insight into collective phenomena in biological membranes. Coarse graining allowed investigation of longer time and length scales by reducing the degrees of freedom and employing suitable potentials. In this work, membranes that include transmembrane proteins are modelled. This allows one to compare the molecular transport across a lipid membrane with and without the assistance of transmembrane channels. Outer membrane protein A (OmpA) – a porin from Escherichia coli with a small pore size – was chosen in this study because its detailed structure is known, it has high stability and is known to form a nonspecific diffusion channel that permits the penetration of various solutes. In this work the pore characteristics and interaction between lipid and protein were investigated and transport of water and other small gas molecules within the channel were studied. The MD simulation results obtained are compared with previous simulation results and available experimental data. The results obtained from this study will lead to better understanding of protein functionality and advance the development of biochips and drug delivery systems.     

Molecular dynamics simulation of pervaporation in zeolite membranes

The pervaporation separation of liquid mixtures of water/ethanol and water/methanol using three zeolite (Silicalite, NaA and Chabazite) membranes has been examined using the method of molecular dynamics. The main goal of this study was to identify intermolecular interactions between water, methanol, ethanol and the membrane surface that play a critical role in the separations. This would then allow better membranes to be designed more efficiently and systematically than the trial-and-error procedures often being used. Our simulations correctly exhibited all the qualitative experimental observations for these systems, including the hydrophobic or hydrophilic behaviour of zeolite membranes. The simulations showed that, for Silicalite zeolite, the separation is strongly influenced by the selective adsorption of ethanol. The separation factor, as a consequence, increases almost exponentially as the ethanol composition decreases. For ethanol dehydration in NaA and Chabazite, pore size was found to play a very important role in the separation; very high separation factors were therefore possible. Simulations were also used to investigate the effect of pore structure, feed compositions and operating conditions on the pervaporation efficiency. Finally, our simulations also demonstrated that molecular simulations could serve as a useful screening tool to determine the suitability of a membrane for potential pervaporation separation applications. Simulations can cost only a small fraction of an experiment, and can therefore be used to design experiments most likely to be successful.     

The role of polarization of Xe by di- and monovalent cations in Xe NMR studies in zeolite A

We consider the role of polarization in the adsorption of Xe in zeolites of type A by direct comparative analysis of the adsorption isotherms, distributions of occupancies, and ¹²⁹Xe NMR chemical shifts of Xe_n in cages containing Ca_xNa_{12 −2x} ions per alpha cage (x = 0, 1, 2, 3, 5). We find that the qualitative trends in the adsorption isotherms, and in the progressions of Xe_n chemical shifts (for n = 0–8 in cages with x = 0, 1 Ca²⁺ ions and for n = 0–5 in cages with x = 2, 3 Ca²⁺ ions) upon increasing the level of Ca²⁺ ion for Na⁺ ion substitution could only be accounted for by including polarization of the Xe atom by the zeolite framework and its ions. This system, which permits observation of individual Xe_n peaks and of directly comparable adsorption isotherms in several cage types, provides a good model system for the interpretation of the more general case in which only the overall average ¹²⁹Xe NMR chemical shift is observed in open network zeolites, arising from free exchange of Xe among cavities of variable occupancy and variable cation distribution.     

The cracking of n-heptane in the gas phase state and in the HZSM-5 zeolite: a quantum molecular dynamics study

Quantum molecular dynamics is used to investigate the cracking of a representative hydrocarbon of the paraffin family (n-heptane), analysing the effects of temperature in the fragmentation of n-heptane when this compound is in the gas phase and inside a typical industrial catalyst (zeolite HZSM-5). The hydrocarbon structural and electronic features in the two environments are determined and compared. The results substantiate current views and exhibit the basic aspects in the cracking of n-heptane.     

Single-particle and collective dynamics of protein hydration water: a molecular dynamics study

We present an analysis based on molecular dynamics simulations of water single particle and collective density fluctuations in a protein crystal at 150 and 300 K. For the collective dynamics, the calculations predict the existence of two sound modes. The first one around 35 meV is highly dispersive and the second one around 9 meV is weakly dispersive in the k range studied here (0.5相似文献   

Xenon matrix and zeolite Na-Y two methods for study of radical cations

Two new methods for the study of reactive radical cations are outlined. The commonly used freon matrix method for the study of radical cations produced by the γ- radiolysis is augmented by the use of a xenon matrix with an electron scavenger. The use of a zeolite matrix is a new development as the zeolite structure, and the ions in the zeolite can be utilized to stabilize radiolytically produced cations in a remarkable temperature range.     

Relaxation dynamics and power spectra of liquid water: a molecular dynamics simulation study

We present molecular dynamics simulations of liquid water at normal and supercooled conditions. Autocorrelation functions (ACFs) of several structural quantities and their fourier transforms are obtained and analysed. Structural correlations and relaxation times increase linearly with degree of supercooling. Power spectra of ACFs show increase in librational motion of liquid water with cooling. These modes intensify with supercooling because of structuring and ordering of water molecules. Overall, liquid water structure is homogenous over the temperatures and pressures studied and undergoes fluctuation–dissipation in its local-density variations [English and Tse, Phys. Rev. Lett. 106, 037801 (2011)].     

Conformational properties of cyclooctane: a molecular dynamics simulation study

Atomistic molecular dynamics simulations have been used to elucidate the conformational properties of cyclooctane in the gas and bulk liquid phases. Accurate reproduction of the gas phase structure, and of the liquid phase densities and solubility parameters have been used as prerequisites to the prediction of conformational properties. The gas phase results clearly indicate the presence of a conformational mixture consisting of the crown, boat-chair, twist-boat-chair and boat-boat conformers at all temperatures (161, 313 and 400 K) studied. The fraction of the crown family of conformers was found to be relatively insensitive to temperature. However, the relative concentrations of the twist-boat-chair and boat-chair conformations was found to be highly temperature dependent with the boat-chair being favoured at low temperatures. Bulk packing was found to have a profound effect on the conformational properties in the liquid phase. At the temperatures studied (313 and 400 K) the boat-chair family was predominant, with the crown and boat families being essentially absent. The twist-boat-chair conformation was detected in the liquid phase at both temperatures. The pseudorotation pathway for the twist-boat-chair to boat-chair interconversion was prevalent in both gas and liquid phases establishing the conformational flexibility and the relative importance of the twist-boat-chair conformer in comparison to the crown family. The study successfully explains the separate experimental findings in both the gas and liquid phases of cyclooctane.     

Estimation of slow diffusion rates in confined systems: CCl4 in zeolite NaA

Often the rate of passage of gaseous molecules through model zeolites is too small to be computed directly. An estimate for the rate of passage of CCl₄ through the 8-ring window in a model of zeolite A has been obtained by combining a direct evaluation of the free energy profile and an adaptation of the rare events method. First the free energy profile is found from a direct evaluation of the canonical partition function at high dilution and the transition state theory rate constant obtained. The dynamic correction factor is then estimated from molecular dynamics runs and used to compute the actual rate k_eff. The method is used to estimate the rate of passage through the 8-ring window in a rigid model of zeolite A, and the results are compared with those obtained from rigid models with expanded windows and from the flexible model. Even a small expansion in the 8-ring window diameter increases the rate significantly, but the changes associated with a flexible cage are small.     

A molecular dynamics study of the swelling patterns of Na/Cs-montmorillonites and the hydration of interlayer cations

We report on a molecular dynamics study of the swelling patterns of an Na-rich/Cs-poor montomorillonite and a Csmontomorillonite.The recently developed CLAYFF force field is used to predict the basal spacing as a function of the water content in the interlayer.The simulations reproduce the swelling patterns of the Na and Cs-montomorillonite,suggesting a mechanism of its hydration different from that of the montomorillonite.In addition,we find that the differences in size and hydration energy of Na and Cs ions have strong implications for the structure and the internal energy of interlayer water.In particular,our results indicate that the hydrate difference in the presence of coexistent Na and Cs has a larger influence on the behavior of a clay-water system.For Na-rich/Cs-poor montomorillonite,the hydration energy values of Na ions and water molecules each have a dramatic increase compared with those in Na-montomorillonite on the interlayer spacing,and the hydration energy values of Cs ions and water molecules decrease somewhat compared with those in Cs-montomorillonite.     

Platinum nanoclusters on graphite substrates: a molecular dynamics study

Molecular dynamics simulations are used to investigate the shape and structure evolution of single platinum clusters of cubic and spherical shape containing 256 and 260 atoms, respectively, deposited on a static graphite substrate. The evolution is monitored at variable temperature, and as a function of metal-substrate interactions at constant temperature. The Pt-Pt interactions are modelled with the many-body Sutton-Chen potential, whereas a Lennard-Jones potential is used to describe the Pt-C interactions. Heating and cooling curves calculated between 200 K and 1800 K are used to determine solid-solid and solid-liquid transitions. Structural changes are detected through analyses of density profiles and diffusion coefficients. A clear analogy is observed between temperature-induced wetting phenomena and those resulting from enhancement of the metal-substrate interactions.     

Probing location of cations responsible for adsorption behavior of zeolite molecular sieve-A using electron spectroscopy

X-ray photoelectron spectroscopy (XPS) has been used to probe surface cations of A-type molecular sieves. Surface compositional data and binding energies of external framework atoms helped in identifying location of cations (site II) responsible for adsorption behavior of molecular sieves. A correlation of carbon dioxide and water adsorption behavior with concentration of probed cations has been made for Na-A and cesium-exchanged A-type molecular sieves.     

纳米多晶铜的超塑性变形机理的分子动力学探讨

在聚能装药爆炸压缩形成射流的过程中, 伴随着金属药型罩的晶粒细化, 从原始晶粒30-80 μm细化到亚微米甚至纳米量级, 从微观层面研究其细化机理和动态超塑性变形机理具有很重要的科学意义. 采用分子动力学方法模拟了不同晶粒尺寸下纳米多晶铜的单轴拉伸变形行为, 得到了不同晶粒尺寸下的应力-应变曲线, 同时计算了各应力-应变曲线所对应的平均流变应力. 研究发现平均流变应力最大值出现在晶粒尺寸为14.85 nm时. 通过原子构型显示, 给出了典型的位错运动过程和晶界运动过程, 并分析了在不同晶粒尺寸下纳米多晶铜的塑性变形机理. 研究表明: 当晶粒尺寸大于14.85 nm时, 纳米多晶铜的变形机理以位错运动为主; 当晶粒尺寸小于14.85 nm时, 变形机理以晶界运动为主, 变形机理的改变是纳米多晶铜出现软化现象即反常Hall-Petch关系的根本原因. 通过计算结果分析, 建立了晶粒合并和晶界转动相结合的理想变形机理模型, 为研究射流大变形现象提供微观变形机理参考.     

Femtosecond laser ablation of metals:a molecular dynamics simulation study

Using molecular dynamics (MD) methods combining with two-step radiation heating model, the mechanisms of ablation and the thermodynamic states at Ni surface under femtosecond laser irradiation are investigated. Simulation results show that the main mechanisms of ablation are evaporation and tensile stresses generated inside the target. The velocity of stress wave is predicted to be nearly equal to sound velocity. The rates of ablation at different fluences obtained from simulations are in good agreement with experimental data. Superheating phenomenon is also discovered.     

Acetonitrile revisited: a molecular dynamics study of the liquid phase

The subject of this report is the calibration of a model of the liquid state of acetonitrile (methyl cyanide). The model describes the liquid in terms of molecular mechanics with each molecule of the liquid treated as a rigid body that is composed of three interaction sites, between which Coulomb and dispersion interactions are computed. A brief overview of the literature on such models is given and a set of parameters for the model is presented. The representation of liquid acetonitrile produced by the parameters is compared to that produced by several other parameter sets available in the literature. It is concluded that, of the parameter sets for the three-site molecular mechanics model that currently are available, under the simulation conditions used, the one presented produces the most rounded representation of the properties of liquid acetonitrile.     

Manipulation of biomolecules: A molecular dynamics study

With the rapid progression of bionanorobotics, manipulation of nano-scale biosamples is becoming increasingly attractive for different biological purposes. Nevertheless, the interaction between a robotic probe and a biological sample is poorly understood and the conditions for appropriate handling is not well-known. Here, we use the molecular dynamics (MD) simulation method to investigate the manipulation process when a nanoprobe tries to move a biosample on a substrate. For this purpose, we have used Ubiquitin (UBQ) as the biomolecule, a single-walled carbon nanotube (SWCNT) as the manipulation probe, and a double-layered graphene sheets as the substrate. A series of simulations were conducted to study the effects of different conditions on the success of the manipulation process. These conditions include the tip diameter, the vertical gap between the tip and substrate, and the initial orientation of the protein. Also we have studied two strategies for the manipulation of the protein by a nano-scale probe that we have named pushing and pulling. Interaction force between carbon nanotube (CNT) tips and the biomolecule, the root-mean-square deviation (RMSD), and the radius of gyration of the protein are monitored for different conditions. We found that larger tip diameters, smaller gaps between tip and substrate, and a pulling strategy increase the chance of a successful manipulation.     

Dielectrophoresis of nanocolloids: A molecular dynamics study

Dielectrophoresis (DEP), the motion of polarizable particles in non-uniform electric fields, has become an important tool for the transport, separation, and characterization of microparticles in biomedical and nanoelectronics research. In this article we present, to our knowledge, the first molecular dynamics simulations of DEP of nanometer-sized colloidal particles. We introduce a simplified model for a polarizable nanoparticle, consisting of a large charged macroion and oppositely charged microions, in an explicit solvent. The model is then used to study DEP motion of the particle at different combinations of temperature and electric field strength. In accord with linear response theory, the particle drift velocities are shown to be proportional to the DEP force. Analysis of the colloid DEP mobility shows a clear time dependence, demonstrating the variation of friction under non-equilibrium. The time dependence of the mobility further results in an apparent weak variation of the DEP displacements with temperature.     

Brine rejection from freezing salt solutions: a molecular dynamics study

The atmospherically and technologically very important process of brine rejection from freezing salt solutions is investigated with atomic resolution using molecular dynamics simulations. The present calculations allow us to follow the motion of each water molecule and salt ion and to propose a microscopic mechanism of brine rejection, in which a fluctuation (reduction) of the ion density in the vicinity of the ice front is followed by the growth of a new ice layer. The presence of salt slows down the freezing process, which leads to the formation of an almost neat ice next to a disordered brine layer.