Molecular simulation of adsorption of alkanes in sodium MOR-type zeolites using a new force field

The applicability of a recently proposed force field of Calero et al. (J. Am. Chem. Soc., 2004, 126, 11377) to Na-MOR zeolites is evaluated. The Henry law coefficients of ethane and C(5)-C(9) as well as the adsorption isotherms of ethane, propane, butane, and hexane in various Na-MOR zeolites are computed and compared with experimental values. These comparisons show that the new force field is suitable for Na-MOR zeolites. Furthermore, this force field is used to study the effects of sodium cations on the adsorption behavior of larger alkanes, such as C(4)-C(7), in MOR-type zeolites. These simulations give a better understanding of the underlying mechanisms of the cations' position and density influence on adsorption. In addition, a characteristic pressure named "reversal pressure" is introduced which characterizes the efficiency of the presence of cations in zeolites.     

Understanding the role of sodium during adsorption: a force field for alkanes in sodium-exchanged faujasites

We have developed a united atom force field able to accurately describe the adsorption properties of linear alkanes in the sodium form of FAU-type zeolites. This force field successfully reproduces experimental adsorption properties of n-alkanes over a wide range of sodium cation densities, temperatures, and pressures. The force field reproduces the sodium positions in dehydrated FAU-type zeolites known from crystallography, and it predicts how the sodium cations redistribute when n-alkanes adsorb. The cations in the sodalite cages are significantly more sensitive to the n-alkane loading than those in the supercages. We provide a simple expression that adequately describes the n-alkane Henry coefficient and adsorption enthalpy as a function of sodium density and temperature at low coverage. This expression affords an adequate substitute for complex configurational-bias Monte Carlo simulations. The applicability of the force field is by no means limited to low pressure and pure adsorbates, for it also successfully reproduces the adsorption from binary mixtures at high pressure.     

Polarizable empirical force field for alkanes based on the classical Drude oscillator model

Recent extensions of potential energy functions used in empirical force field calculations have involved the inclusion of electronic polarizability. To properly include this extension into a potential energy function it is necessary to systematically and rigorously optimize the associated parameters based on model compounds for which extensive experimental data are available. In the present work, optimization of parameters for alkanes in a polarizable empirical force field based on a classical Drude oscillator is presented. Emphasis is placed on the development of parameters for CH3, CH2, and CH moieties that are directly transferable to long chain alkanes, as required for lipids and other biomolecules. It is shown that a variety of quantum mechanical and experimental target data are reproduced by the polarizable model. Notable is the proper treatment of the dielectric constant of pure alkanes by the polarizable force field, a property essential for the accurate treatment of, for example, hydrophobic solvation in lipid bilayers. The present alkane force field will act as the basis for the aliphatic moieties in an extensive empirical force field for biomolecules that includes the explicit treatment of electronic polarizability.     

Effects of confinement on the adsorption behavior of methane in high-silica zeolites

Adsorption isotherms of methane on high-silica zeolites at ambient temperature and up to high pressure were experimentally measured. The isotherms were analyzed on the basis of thermodynamics and statistical mechanics, and the relationship between microscopic properties and the macroscopic adsorption behavior was investigated. A comparison between the confined and unconfined phases revealed that molecular motion is restricted in the pores. As a result, the adsorbed phase is entropically destabilized, which cannot be neglected in comparison with the energetical stabilization that occurs as a result of the solid-molecule interaction. Our findings also indicate that the smaller slope (drho/d ln p) of the adsorption isotherms compared to that of the isotherm of the bulk at the same density is due to the smaller intermolecular interaction in the pores.The pore-size dependence is indicated not only in solid-molecule interactions but also in intermolecular interactions and molecular motion. Of these, the solid-molecule interactions strongly influence the adsorption behaviors in pores of different sizes. The origin of the restriction of molecular motion in the pores is well-explained by the one-dimensional transition and two-dimensional vibration (1D-trans, 2D-vib) model.     

Theoretical description of the adsorption and the wetting behavior of alkanes on water

The wetting behavior of alkanes of medium chain length (e.g., pentane, hexane, and heptane) on water is more complex than the usually observed first-order wetting transition from partial to complete wetting by showing a sequence of two transitions. In this sequential-wetting scenario, a first-order transition from a microscopically thin to a mesoscopically thick layer of liquid on the substrate surface is followed by a continuous divergence of the film thickness upon increase of the temperature. This critical transition to complete wetting at T(w,c) is solely determined by long-range interactions between substrate and adsorbate, which are well-described by Dzyaloshinskii-Lifshitz-Pitaevskii [Adv. Phys. 10, 165 (1961)] theory in terms of the static dielectric constants and the refractive indices of the media involved. The first-order thin-thick transition, however, which occurs at a lower temperature T(w,1), results from an interplay of short-range and long-range forces and is notoriously more difficult to describe because a satisfactory theory of the short-range interactions between substrate and adsorbate is still missing. The approach presented in this paper attempts to account for the short-range interactions in an effective way: Within a Cahn-type [J. Chem. Phys. 66, 3667 (1977)] theory that has been augmented for long-range interactions and modified to treat the first layer of adsorbed molecules in a lattice-gas approach, the contact energy is deduced from the surface pressure, which in turn is calculated using a two-dimensional van der Waals equation of state and an expression for the Henry's law constant that was derived by Hirasaki [J. Adhes. Sci. Technol. 7, 285 (1993)]. The method uses only the dielectric properties of the isolated bulk media and simple assumptions on the size and the shape of the adsorbed alkane molecules and leads to satisfactory results for the transition temperatures T(w,1) and T(w,c).     

Comparison of various models describing the adsorption of surfactant molecules capable of interfacial reorientation

The thermodynamic model for describing the adsorption of surfactant molecules in different adsorption states, the reorientation model, is reconsidered on a more rigorous level. The resulting model equations are used to describe experimental surface pressure data published in the literature. The new model proposed contains three physical parameters and describes the experimental dependencies Pi(c) for oxethylated alcohols very accurately.     

Aminopropyl-grafted various silica mesostructures for adsorption of molybdenum ions from Re-containing effluent

Four different silica mesostructures, SBA-15 with mesopore size (8.5 nm), SBA-15 with mesopore size (10.3 nm), mesocellular foam (MCF) with uniform cell size (33.2 nm), and MCF with bimodal mesoporosity, were grafted with aminopropyl groups and used for selective recovery of Mo(VI) from Re(VII)-containing effluent. Adsorption isotherms and mechanism of Mo(VI) adsorption on these materials were studied. The adsorbed complexes of Mo(VI) could be formed by ion exchange process or/and by chelation reaction. This study shows a new approach for fractional recovery and separation of Mo(VI) from Re(VII) by using amino-modified SBA-15-type mesoporous silica.     

Modelling adsorption of a water molecule into various pore structures of silica gel

Silica gel is widely used in commercial applications as a water adsorbent due to its properties including hydrothermally stable, high water sorption capacity, low regeneration temperature, low cost and wide range of pore diameters. Since the water sorption capacity of silica gel strongly depends on the pore size and structure, which can be controlled during synthesis, this paper study the effect of pore shapes and dimensions of silica gel upon the adsorption of a water molecule aiming at maximising the water sorption capacity. In particular, we consider three types of pore structures, namely cylindrical, square prismatic and conical pores. On using the Lennard-Jones potential and a continuum approximation, we find that the minimum radii for a water molecule to be accepted into cylindrical, square prismatic and conical pores are 4.009, 3.7898 and 4.4575 Å, respectively. For cylindrical and square prismatic pores, the critical radii which maximise the adsorption energy are 4.5189 and 4.1903 Å, respectively. Knowledge of these critical pore sizes may be useful for the manufacturing process of silica gel that will maximise the water sorption capacity.     

Accurate van der Waals force field for gas adsorption in porous materials

An accurate van der Waals force field (VDW FF) was derived from highly precise quantum mechanical (QM) calculations. Small molecular clusters were used to explore van der Waals interactions between gas molecules and porous materials. The parameters of the accurate van der Waals force field were determined by QM calculations. To validate the force field, the prediction results from the VDW FF were compared with standard FFs, such as UFF, Dreiding, Pcff, and Compass. The results from the VDW FF were in excellent agreement with the experimental measurements. This force field can be applied to the prediction of the gas density (H₂, CO₂, C₂H₄, CH₄, N₂, O₂) and adsorption performance inside porous materials, such as covalent organic frameworks (COFs), zeolites and metal organic frameworks (MOFs), consisting of H, B, N, C, O, S, Si, Al, Zn, Mg, Ni, and Co. This work provides a solid basis for studying gas adsorption in porous materials. © 2017 Wiley Periodicals, Inc.     

Development of an empirical force field for silica. Application to the quartz-water interface

Interactions of pulverized crystalline silica with biological systems, including the lungs, cause cell damage, inflammation, and apoptosis. To allow computational atomistic modeling of these pathogenic processes, including interactions between silica surfaces and biological molecules, new parameters for quartz, compatible with the CHARMM empirical force field were developed. Parameters were optimized to reproduce the experimental geometry of alpha-quartz, ab initio vibrational spectra, and interactions between model compounds and water. The newly developed force field was used to study interactions of water with two singular surfaces of alpha-quartz, (011) and (100). Properties monitored and analyzed include the variation of the density of water molecules in the plane perpendicular to the surface, disruption of the water H-bond network upon adsorption, and space-time correlations of water oxygen atoms in terms of Van Hove self-correlation functions. The vibrational density of states spectra of water in confined compartments were also computed and compared with experimental neutron-scattering results. Both the attenuation and shifting to higher frequencies of the hindered translational peaks upon confinement are clearly reproduced by the model. However, an upshift of librational peaks under the conditions of model confinement still remains underrepresented at the current empirical level.     

Conformation of alkanes in the gas phase and pure liquids

Monte Carlo (MC) statistical mechanics simulations have been carried out for the homologous alkane series of n-butane through n-dodecane in the gas phase and for the pure liquids at 298 K and 1 atm using the OPLS-AA force field. The study addresses potential cumulative deviations of computed properties and potential conformational differences between the gas phase and pure liquids, for example, from self-solvation in the gas phase. The average errors in comparison with experimental data for the computed densities and heats of vaporization are modest at 0.7% and 6.9%, respectively. Also, the invariant gas and liquid-phase results for average end-to-end distances and percentages of trans conformations for each nonterminal C-C bond assert that the conformer populations are not altered upon transfer from the gas phase to the pure liquid for the n-alkanes in this size range. Average end-to-end distances were also computed from the results of conformational searches and corroborated the MC findings. Quantitatively, the OPLS-AA result for the trans population of the C3-C4 bond in n-undecane is in close agreement with the findings from (13)C NMR experiments. Finally, previous work on determining the shortest n-alkane that does not have an all-trans global energy minimum has been extended. The smallest n-alkane with a hairpin geometry that is lower in energy than the all-trans conformer occurs for C(22)H(46) with OPLS-AA, though with a correction for GG sequences, the true turning point is likely in the C(16)-C(18) range.     

The SAAP force field. A simple approach to a new all-atom protein force field by using single amino acid potential (SAAP) functions in various solvents

A simple strategy to compose a new all-atom protein force field (named as the SAAP force field), which utilizes the single amino acid potential (SAAP) functions obtained in various solvents by ab initio molecular orbital calculation applying the isodensity polarizable continuum model (IPCM), is presented. We considered that the total energy function of a protein force field (E(TOTAL)) is divided into three components; a single amino acid potential term (E(SAAP)), an interamino acid nonbonded interaction term (E(INTER)), and a miscellaneous term (E(OTHERS)), which is ignored (or considered to be constant) at the current version of the force field. The E(INTER) term consists of electrostatic interactions (E(ES')) and van der Waals interactions (E(LJ')). Despite simplicity, the SAAP force field implicitly involves the correlation among individual terms of the Lifson's potential function within a single amino acid unit and can treat solvent effects unambiguously by choosing the SAAP function in an appropriate solvent and the dielectric constant (D) of medium. Application of the SAAP force field to the Monte Carlo simulation of For-Ala(2)-NH(2) in vacuo reasonably reproduced the results of the extensive conformational search by ab initio molecular orbital calculation. In addition, the preliminary Monte Carlo simulations for For-Gly(10)-NH(2) and For-Ala(10)-NH(2) showed reversible transitions from the extended to the pseudosecondary structures in water (D = 78.39) as well as in ether (D = 4.335). The result suggested that the new approach is efficient for fast modeling of protein structures in various environments. Decomposition analysis of the total energy function (E(TOTAL)) by using the SAAP force field suggested that conformational propensities of single amino acids (i.e., the E(SAAP) term) may play definitive roles on the topologies of protein secondary structures.     

Analytical models for describing cation adsorption/desorption kinetics as considering the electrostatic field from surface charges of particles

Surface charges of particles together with the adsorbed counter ions in diffuse layer can set up a strong electrostatic field around the particles in aqueous solution. The existent kinetic models for describing cation exchange on solid/liquid interface were either empirical or semi-empirical, and in which the electrostatic field is not considered. In this paper, as considering the important effect of electrostatic field around particles on cations adsorption/desorption, for the first time the dynamic distribution equations of cations in diffuse layer for adsorption and desorption processes in both flow method and batch technique have been established. Those equations clearly show how the cation concentration changes with time in different position of diffuse layer during the cation exchange process, and the corresponding new kinetic models have been obtained upon them. The new models indicate that, in both flow method and batch technique, for the adsorption process, experimental results should appear zero order kinetic process caused by the strong force adsorption in the initial stage of adsorption, and then transform to the first order kinetic process of the weak force adsorption; and for the desorption process, however, only first order kinetic process may exist. The new models are essentially different from the classic apparent or empirical kinetic models since all the parameters have their defined physical meanings in the new models, thus the rate parameters in the new models have the potential to theoretically predict. Theoretical analyses also indicated that, the adsorption/desorption rate in flow method experiment will be much higher than that in batch technique experiment.