Spontaneous segregation on a hybrid chiral surface

Segregation of enantiomers in two-dimensional adsorbed layers is a process that is usually controlled by anisotropic directional interactions between adsorbed molecules. In this contribution, we propose a simple theoretical model in which the chiral segregation occurs even though the lateral interactions are neglected. In particular, we consider a solid surface composed of two domains with different patterns of active sites being mirror images of each other. The domains of opposite handedness represent crystal facets of a composite chiral material which are adjoined to form a heterochiral adsorbing surface. To explore equilibrium properties of the system, we use Canonical Ensemble Monte Carlo method for a square lattice. The influence of factors such as energetic properties of the surface and density of the adsorbed layer on the extent of separation is examined. The obtained results indicate that effective two-dimensional separation on the hybrid chiral surface assumed in our model can be achieved only at sufficiently low adsorbate densities. The results also suggest that the segregation on the hybrid surface would be a promising method of enantiodiscrimination for those chiral molecules which do not exhibit strong lateral interactions.     

Porous nanotube network: a novel 3-D nanostructured material with enhanced hydrogen storage capacity

A multiscale theoretical approach (ab initio and Grand Canonical Monte Carlo calculations) was used to investigate hydrogen storage in a novel three-dimensional carbon nanostructure. Our results show that a large-pore PNN can overpass the gravimetric capacity of 20% at 77 K while a Li-doped PNN can reach the value of 8% at room temperature.     

Salen-Based Conjugated Microporous Polymers for Efficient Oxygen Evolution Reaction

Exploring high-performance electrocatalysts, especially non-noble metal electrocatalysts, for the oxygen evolution reaction (OER) is critical to energy storage and conversion. Herein, we report for the first time that conjugated microporous polymers (CMPs) incorporating salen can be used as OER electrocatalysts with outstanding performances. The best OER electrocatalyst (salen-CMP-Fe-3) exhibits a low Tafel slope of 63 mV dec⁻¹ and an overpotential of 238 mV at 10 mA cm⁻². DFT and Grand Canonical Monte Carlo calculations confirmed that the significantly improved electrocatalytic properties can be attributed to the intrinsic catalytic activity of the salen moiety and the enrichment effect of the pore structures. This work demonstrates that salen-based conjugated polymers are a type of metal-coordinated porous polymer that show excellent catalyst performance.     

On the breathing effect of a metal-organic framework upon CO(2) adsorption: Monte Carlo compared to microcalorimetry experiments

Grand Canonical Monte Carlo simulations have explained the breathing of a metal-organic framework upon CO(2) adsorption, first suggested by microcalorimetry.     

Water adsorption in disordered mesoporous silica (Vycor) at 300 K and 650 K: a Grand Canonical Monte Carlo simulation study of hysteresis

This numerical simulation paper focuses on the adsorption/desorption of water in disordered mesoporous silica glasses (Vycor-like). The numerical adsorbent was previously obtained by off lattice method, and was shown to reproduce quite well the micro- and mesotextural properties of real Vycor, as well as morphological (pore size distribution) and topological (pore interconnections) disorder. The water-water interactions are described by the SPC model while water-silica interactions are calculated in the framework of the PN-TrAZ model. The water adsorption/desorption isotherms and the configurational energies are calculated by the Grand Canonical Monte Carlo simulation method. The low pressure results compare well with experiments, showing the good transferability of the intermolecular potential. It is shown that if the hysteresis loop observed in the adsorption/desorption isotherm is considered as a true phase transition (which is actually still an open question in the case of disordered porous materials), then it is possible to calculate the grand potential by applying the thermodynamic integration scheme. The grand potential is shown to be multivalued for low (subcritical) temperature, and continuous for high (supercritical) temperature. A coexistence point is found within the hysteresis loop, actually close to the vertical desorption line. Below the equilibrium chemical potential, the gaslike branch is stable whereas the liquidlike branch is metastable. The situation is reversed above the coexistence point.     

On the theory of the rupture of black films

The present work covers the solution of a problem on the fluctuation rupture of black films [Derjaguin, B.V., and Gutop, Yu. V., Kolloid. zh. 24, 431 (1962); Dokl. AN SSSR 153, 859 (1963); “Research in Surface Forces,” Vol. 2, p. 36. Consultants Bureau, New York, 1966], which is interpreted as a two-dimensional analog of the homogeneous boiling of fluid. Such a two-dimensional mechanism of rupture must be realized first of all for secondary black and lipid films. Using the solution of the stationary Kramers-Zeldovich equation as the basis, we have derived a general expression for the probability of the isothermal rupture of a stretched film of the given area per unit time. The use of Gibbs Grand Ensemble [Derjaguin, B.V., Zh. eksp. teor. fis. 65, 2261 (1973); J. Chem. Phys. 61, 3665 (1974)] enabled us to calculate accurately the pre-exponential factor in that expression. Criteria of the applicability of the results obtained have been determined. A possibility is discussed for applying the abrupt dependence of the rupture probability of a film on its linear tension, to the accurate measurement of the latter.     

Histogram analysis as a method for determining the line tension of a three-phase contact region by Monte Carlo simulations

A method is proposed for determining the line tension, which is the main physical characteristic of a three-phase contact region, by Monte Carlo (MC) simulations. The key idea of the proposed method is that if a three-phase equilibrium involves a three-phase contact region, the probability distribution of states of a system as a function of two order parameters depends not only on the surface tension, but also on the line tension. This probability distribution can be obtained as a normalized histogram by appropriate MC simulations, so one can use the combination of histogram analysis and finite-size scaling to study the properties of a three phase contact region. Every histogram and results extracted therefrom will depend on the size of the simulated system. Carrying out MC simulations for a series of system sizes and extrapolating the results, obtained from the corresponding series of histograms, to infinite size, one can determine the line tension of the three phase contact region and the interfacial tensions of all three interfaces (and hence the contact angles) in an infinite system. To illustrate the proposed method, it is applied to the three-dimensional ternary fluid mixture, in which molecular pairs of like species do not interact whereas those of unlike species interact as hard spheres. The simulated results are in agreement with expectations.     

The effect of nanopore shape on the structure and isotherms of adsorbed fluids

A Grand Canonical Monte Carlo simulation method is used to determine the adsorption isotherms, interaction energies, entropies, and density distribution of a Lennard-Jones fluid adsorbed in smooth-walled nanopores of varying size and shape. We specifically include very crowded pores, where packing effects are important. Differences in the isotherms of slit, cylindrical, and spherical nanopores of varying sizes can be explained in terms of the adsorbate-adsorbate interaction energy, the adsorbate-pore interaction energy, and the density profiles, which influence the balance between the former and the latter energy contributions. The expectation from low loading studies that the most energetically favorable adsorbate-pore interactions maximize adsorption is not borne out at intermediate and higher loadings. Instead, the relationships between adsorbed amounts and pore size and shape are found to be strong functions of the depth and steepness of the external potential, the extent to which adsorbate-adsorbate repulsion establishes short range fluid order, and the accessible pore volume. This study has implications for high pore density processes in nanoporous materials, such as zeolite catalysis, separations, and templating in zeolite synthesis.     

The effects of energy sites on adsorption of Lennard-Jones fluids and phase transition in carbon slit pore of finite length a computer simulation study

A Monte Carlo simulation method is used to study the effects of adsorption strength and topology of sites on adsorption of simple Lennard-Jones fluids in a carbon slit pore of finite length. Argon is used as a model adsorbate, while the adsorbent is modeled as a finite carbon slit pore whose two walls composed of three graphene layers with carbon atoms arranged in a hexagonal pattern. Impurities having well depth of interaction greater than that of carbon atom are assumed to be grafted onto the surface. Different topologies of the impurities; corner, centre, shell and random topologies are studied. Adsorption isotherms of argon at 87.3 K are obtained for pore having widths of 1, 1.5 and 3 nm using a Grand Canonical Monte Carlo simulation (GCMC). These results are compared with isotherms obtained for infinite pores. It is shown that the surface heterogeneity affects significantly the overall adsorption isotherm, particularly the phase transition. Basically it shifts the onset of adsorption to lower pressure and the adsorption isotherms for these four impurity models are generally greater than that for finite pore. The positions of impurities on solid surface also affect the shape of the adsorption isotherm and the phase transition. We have found that the impurities allocated at the centre of pore walls provide the greatest isotherm at low pressures. However when the pressure increases the impurities allocated along the edges of the graphene layers show the most significant effect on the adsorption isotherm. We have investigated the effect of surface heterogeneity on adsorption hysteresis loops of three models of impurity topology, it shows that the adsorption branches of these isotherms are different, while the desorption branches are quite close to each other. This suggests that the desorption branch is either the thermodynamic equilibrium branch or closer to it than the adsorption branch.     

The Grand Canonical Monte Carlo Simulations of Benzene and Propylene in ITQ-1 Zeolite

Thealkylationofbenzenewithpropylenetoproducecumene,astartingmaterialfortheproductionofacetoneandphenol,isveryimportantinhydrocarbonprocess.ComparedwithsomemineralacidsincludingAlCl,andothers,zeolitesseemtobemorecleancatalysts,moreoveF,theycaneffectivelyreducetheamountoflessdesiredproductssuchasdiisopropylbenzenes.SeveralzeoIitesincludingH-ZSM-5,USYflandMCM-22havebeentestedforthereactionoftheaIkylationofbenzenewithpropylene,andithasbeenfoundthatP,USYandMCM-22areveryreactiveI.ZeoIiteMC…     

Statistical mechanical theory for the structure of steady state systems: application to a Lennard-Jones fluid with applied temperature gradient

The constrained entropy and probability distribution are given for the structure that develops in response to an applied thermodynamic gradient, as occurs in driven steady state systems. The theory is linear but is applicable to gradients with arbitrary spatial variation. The phase space probability distribution is also given, and it is surprisingly simple with a straightforward physical interpretation. With it, all of the known methods of equilibrium statistical mechanics for inhomogeneous systems may now be applied to determining the structure of nonequilibrium steady state systems. The theory is illustrated by performing Monte Carlo simulations on a Lennard-Jones fluid with externally imposed temperature and chemical potential gradients. The induced energy and density moments are obtained, as well as the moment susceptibilities that give the rate of change of these with imposed gradient and which also give the fluctuations in the moments. It is shown that these moment susceptibilities can be written in terms of bulk susceptibilities and also that the Soret coefficient can be expressed in terms of them.     

The mesoscopic dynamics of thermodynamic systems

Concepts of everyday use such as energy, heat, and temperature have acquired a precise meaning after the development of thermodynamics. Thermodynamics provides the basis for understanding how heat and work are related and the general rules that the macroscopic properties of systems at equilibrium follow. Outside equilibrium and away from macroscopic regimes, most of those rules cannot be applied directly. Here we present recent developments that extend the applicability of thermodynamic concepts deep into mesoscopic and irreversible regimes. We show how the probabilistic interpretation of thermodynamics together with probability conservation laws can be used to obtain Fokker-Planck equations for the relevant degrees of freedom. This approach provides a systematic method to obtain the stochastic dynamics of a system directly from its equilibrium properties. A wide variety of situations can be studied in this way, including many that were thought to be out of reach of thermodynamic theories, such as nonlinear transport in the presence of potential barriers, activated processes, slow relaxation phenomena, and basic processes in biomolecules, such as translocation and stretching.     

Electrolyte exclusion from charged adsorbent: replica Ornstein-Zernike theory and simulations

Structural and thermodynamic properties of the restrictive primitive model +1:-1 electrolyte solution adsorbed in a disordered charged media were studied by means of the Grand Canonical Monte Carlo simulation and the replica Ornstein-Zernike theory. Disordered media (adsorbent, matrix) was represented by a distribution of negatively charged hard spheres frozen in a particular equilibrium distribution. The annealed counterions and co-ions were assumed to be distributed within the nanoporous adsorbent in thermodynamic equilibrium with an external reservoir of the same electrolyte. In accordance with the primitive model of electrolyte solutions, the solvent was treated as a dielectric continuum. The simulations were performed for a set of model parameters, varying the net charge of the matrix (i.e., concentrations of matrix ions) and of annealed electrolyte, in addition to the dielectric constant of the invading solution. The concentration of adsorbed electrolyte was found to be lower than the corresponding concentration of the equilibrium bulk solution. This electrolyte "exclusion" depends strongly on the dielectric constant of the invading solution, as also on concentrations of all components. The most important parameter is the net charge of the matrix. Interestingly, the electrolyte rejection decreases with increasing Bjerrum length for the range of parameters studied here. The latter finding can be ascribed to strong inter-ionic correlation in cases where the Bjerumm length is high enough. To a minor extent, the adsorption also depends on the spacial distribution of fixed charges in adsorbent material. The replica Ornstein-Zernike theory was modified to cater for this model and tested against the computer simulations. For the range of parameters explored in this work, the agreement between the two methods is very good. These calculations were also compared with the results of the classical Donnan theory for electrolyte exclusion.     

Optimized expanded ensembles for simulations involving molecular insertions and deletions. II. Open systems

In the Grand Canonical, osmotic, and Gibbs ensembles, chemical potential equilibrium is attained via transfers of molecules between the system and either a reservoir or another subsystem. In this work, the expanded ensemble (EXE) methods described in part I [F. A. Escobedo and F. J. Martinez-Veracoechea, J. Chem. Phys. 127, 174103 (2007)] of this series are extended to these ensembles to overcome the difficulties associated with implementing such whole-molecule transfers. In EXE, such moves occur via a target molecule that undergoes transitions through a number of intermediate coupling states. To minimize the tunneling time between the fully coupled and fully decoupled states, the intermediate states could be either: (i) sampled with an optimal frequency distribution (the sampling problem) or (ii) selected with an optimal spacing distribution (staging problem). The sampling issue is addressed by determining the biasing weights that would allow generating an optimal ensemble; discretized versions of this algorithm (well suited for small number of coupling stages) are also presented. The staging problem is addressed by selecting the intermediate stages in such a way that a flat histogram is the optimized ensemble. The validity of the advocated methods is demonstrated by their application to two model problems, the solvation of large hard spheres into a fluid of small and large spheres, and the vapor-liquid equilibrium of a chain system.     

Nanoscale tubular vessels for storage of methane at ambient temperatures

Novel carbon nanostructures can serve as effective storage media for methane, a source of "clean energy" for the future. We have used Grand Canonical Monte Carlo Simulation for the modeling of methane storage at 293 K and pressures up to 80 MPa in idealized bundles of (10,10) armchair-type single-walled carbon nanotubes and wormlike carbon pores. We have found that these carbon nanomaterials can be treated as the world's smallest high-capacity methane storage vessels. Our simulation results indicate that such novel carbon nanostructures can reach a high volumetric energy storage, exceeding the US FreedomCAR Partnership target of 2010 (5.4 MJ dm(-3)), at low to moderate pressures ranging from 1 to 7 MPa at 293 K. On the contrary, in the absence of these nanomaterials, methane needs to be compressed to approximately 13 MPa at 293 K to achieve the same target. The light carbon membranes composed of bundles of single-walled carbon nanotubes or wormlike pores efficiently physisorb methane at low to moderate pressures at 293 K, which we believe should be particularly important for automobiles and stationary devices. However, above 15-20 MPa at 293 K, all investigated samples of novel carbon nanomaterials are not as effective when compared with compression alone since the stored volumetric energy and power saturate at values below those of the bulk, compressed fluid.     

Determination of the adsorption isotherm of methanol on the surface of ice. An experimental and grand canonical Monte Carlo simulation study

The adsorption isotherm of methanol on ice at 200 K has been determined both experimentally and by using the Grand Canonical Monte Carlo computer simulation method. The experimental and simulated isotherms agree well with each other; their deviations can be explained by a small (about 5 K) temperature shift in the simulation data and, possibly, by the non-ideality of the ice surface in the experimental situation. The analysis of the results has revealed that the saturated adsorption layer is monomolecular. At low surface coverage, the adsorption is driven by the methanol-ice interaction; however, at full coverage, methanol-methanol interactions become equally important. Under these conditions, about half of the adsorbed methanol molecules have one hydrogen-bonded water neighbor, and the other half have two hydrogen-bonded water neighbors. The vast majority of the methanols have a hydrogen-bonded methanol neighbor, as well.     

Application of a single model to study the adsorption kinetics of prednisolone on six carbonaceous materials

The knowledge of the adsorption processes of nonelectrolytes from liquid solution on solid materials involves the study of their kinetic and equilibrium aspects as well as the understanding of their thermodynamic functions. However, in most published papers adsorption isotherms are analyzed by using the Giles classification and other proposed equations which are either empirical or based on kinetic or thermodynamic criteria. Our opinion is that both the kinetic and the equilibrium studies must be complementary and that, in general, equations describing the adsorption isotherms come from the kinetic laws governing the different partial processes which determine the global process. These kinetic laws may be derived from single models. In this paper a single model is proposed, which makes it possible to establish a kinetic law satisfactorily fitting a great number of C (concentration) vs t (time) isotherms. This model has been applied to study the adsorption process of prednisolone by six carbonaceous materials from ethanol solution, the specific adsorption rate, and the activation thermodynamic functions being calculated. The results obtained have also been used to analyze the influence of the intraparticle diffusion on the kinetics of the process.     

Surrogate AutoShim: predocking into a universal ensemble kinase receptor for three dimensional activity prediction, very quickly, without a crystal structure

"Ensemble surrogate AutoShim" is a kinase specific extension of the AutoShim docking method that solves the three traditional limitations of conventional docking: (1) it gives good correlations with affinity, (2) does not require a target protein structure, and (3) for a preprocessed company archive of 1.5 million compounds, is as fast as traditional 2D QSAR. It does require several hundred experimental IC 50 values for each new target. Original AutoShim adds pharmacophore "shims" to a crystal structure binding site. An iterative partial least squares (PLS) procedure selects the best pose, while adjusting the shim weights to reproduce IC 50 data. Surrogate AutoShim adjusts shims in one crystal structure to reproduce IC 50 data for a different kinase target. Ensemble surrogate AutoShim uses 16 structurally diverse kinase crystal structures as a "universal ensemble kinase receptor", suitable for any kinase target. The 1.5 million member Novartis screening collection has been predocked into the shimmed ensemble, so new kinase models can be built, and the entire corporate archive virtually screened, in hours rather than weeks. A kinase-biased set of 10,000 compounds, that samples the entire corporate archive, has been designed for lead discovery by iterative kinase screening.     

狭缝孔内甲烷蒸汽重整化学平衡的分子模拟

采用反应蒙特卡罗方法研究了狭缝孔内甲烷蒸汽重整反应的化学平衡. 模拟中将CH4, CO和H2均描述成球形LJ分子, H2O和CO2分子的势能分别采用TIP4P和EMP2模型计算. 狭缝孔壁与LJ点位之间的相互作用采用Steele的10-4-3模型计算. 由于没有狭缝孔内该反应的实验数据, 因此比较了用经典热力学预测与RCMC方法得到的主体相平衡组成. 两种方法得到的结果比较吻合, 表明采用RCMC方法预测孔内的化学平衡是可靠的. 讨论了其它工艺条件对孔内化学平衡的影响.     

Adsorption of gas mixtures on solid surfaces,theory and computer simulation

A treatment of the thermodynamics of mixed gas adsorption is presented in which the gas-solid interface is three dimensional. Such a treatment yields an additional term as compared to two dimensional approaches. This additional term has significant consequences for the derivation of adsorbed solution theories, particularly at higher temperatures.Results are presented for a Grand Canonical Monte Carlo study of a model methane-ethane mixture in a carbonaceous slit pore. Comparison of single component and mixture results provides an unambiguous means of testing theories of adsorbed solutions and bears out the thermodynamic treatment presented in the previous section of the paper.