Hydrophilicity of Organically Modified Montmorillonite and Effect on Benzene Adsorption by the Molecular Dynamics Method.

Interlayer modification of layered materials with organocations has been known to endow the nanocomposite with hydrophobicity, and adsorption of aromatic compounds in the aqueous phase has been investigated for decades by using montmorillonite, a representative layered clay mineral, as the host material. Usage of the organocation has been believed to be effective due to the π-π interaction with the aromatic adsorbate, the presence of which is not verified spectroscopically in the water-immersed state. Considering that the organocation is generally regarded as a pillar to keep the interlayer space, the interaction between the organocation and adsorbate has not yet been clarified sufficiently. In the present study, we revealed the role of the organocation by the molecular dynamics method, where tetramethylammonium (TMA) and trimethylphenylammonium (TMPA) ions were selected as the representative and simple organocations, and benzene was the adsorbate to exclude the effect of the substitution group. Both H2O and benzene molecules were introduced in the interlayer of TMA- or TMPA-modified montmorillonite to model the water-immersed adsorption structure. It was found that H2O is preferentially distributed on the clay surface, followed by the center of the interlayer when the amount of H2O is large. In the adsorption model, benzene was vertically adsorbed on the clay surface. Radial distribution function analysis revealed that benzene is distributed around both the methyl and the phenyl groups in the TMA and TMPA cations, but the orientation of the phenyl ring is not consistent with that of benzene. Thus, benzene was found not to form the π-π interaction in montmorillonite modified with the TMPA cations in the water-immersed state. Furthermore, the surface was partly covered with the phenyl group in the TMPA cation, decreasing the adsorption area. Therefore, the experimental suggestion that benzene is adsorbed on the clay surface was reproduced by our simulation, and the interaction between the organocation and benzene and surface occupancy should be paid attention to maximize the adsorption property.

Formation and Segregation of a Pd-MgO Solid Solution Studied by X-ray Absorption Spectroscopy.

Thermal treatment of Pd nanoparticles or Pd(NH3)4(NO3)2 supported on MgO resulted in the formation of a solid solution of Pd-MgO, as evidenced by Pd K-edge X-ray absorption fine structure (XAFS). The valence of Pd in the Pd-MgO solid solution was determined to be 4+ from the comparison of X-ray absorption near edge structure (XANES) with reference compounds. A characteristic shrinkage of the Pd-O bond distance was observed in comparison with that of the nearest-neighboring Mg-O bond in MgO, which agreed with the density functional theory (DFT) calculations. The two-spike pattern was observed in the dispersion of Pd-MgO owing to the formation and successive segregation of solid solutions above 1073 K.

High Efficient CO2 Separation at High Pressure by Grain-Boundary-Controlled CHA Zeolite Membrane Investigated by Non-Equilibrium Molecular Dynamics.

The CO2 permeability and selectivity of CHA-type zeolite membranes in the separation of a CO2/CH4 mixture gas at high pressure were evaluated using non-equilibrium molecular dynamics (NEMD). It was found that in a perfectly crystalline, defect-free CHA membrane, the adsorption of CH4, which diffuses slowly in the pores, hinders CO2 permeation. Therefore, an increase in the amount of CH4 adsorbed at high pressure decreases the CO2 permeability and significantly reduces the CO2 selectivity of the CHA membrane. CHA membranes with grain boundaries parallel to the permeation direction were found to show higher CO2 selectivity than perfectly crystalline CHA membranes at high pressure, as the blocking effect of CH4 on CO2 permeation occurring within the grain boundary is not significant. This paper is the first to show that the CO2 permeability of CHA membranes with controlled grain boundaries can exceed the intrinsic performance of fully crystalline zeolite membranes at high pressure.

Estimation of Adsorbed Amounts in Organoclay by Machine Learning.

Adsorption properties of organoclay have been investigated for decades focusing on the morphology and physicochemical properties of two-dimensional interlayers. Experimental studies have previously revealed that the adsorption mechanisms depend on the molecular species of the organocation and adsorbate, making it difficult to estimate the adsorbed amount without experiments. Considering that the adsorption of aromatic compounds has been reported by using various clays, organocations, and adsorbates, machine learning is a promising method to overcome the difficulty. In the present study, we collected adsorption data from the literature and constructed models to estimate the adsorbed amount of the organoclay by random forest regression. The composition of the clay, molecular descriptors of the organocation and adsorbate obtained by the RDKit, and experimental conditions were used as the explanatory variables. Simple model construction by using all the experimental data resulted in low R 2 and a mean absolute error. This problem was solved by the correction of the adsorbed amount data by the Langmuir or Freundlich equation and the following model construction at various equilibrium concentrations. The plots of the adsorbed amount estimated by the latter model were located close to the corresponding adsorption isotherm, while that by the former was not. Thus, it was revealed that the adsorbed amount was estimated quantitatively without understanding the adsorption mechanisms individually. Feature importance analysis also revealed that the combination of the organocation and adsorbate is important at high equilibrium concentrations, while the clay should be selected carefully as the concentration gets lower. Our results give an insight into the rational design of the organoclay including the synthesis and adsorption properties.

Solvent-Solute Interaction Effect on Permeation Flux through Forward Osmosis Membranes Investigated by Non-Equilibrium Molecular Dynamics.

The relationship between the solvent-solute interaction and permeation properties is fundamental in the development of the forward osmosis (FO) membrane. In this study, we report on the quantitative reproduction of the permeation flux, which has different solvent-solute interactions, through the modeled FO membrane by non-equilibrium molecular dynamics (NEMD). The interaction effect was investigated by changing the interatomic interaction between the solute and the solvent. The calculated permeation through the semi-permeable modeled FO membrane, in which the interaction between solvent and solution is equal to that between solutions, was consistent with the theoretical curve derived from the combination of the permeation flux and Van't Hoff equations. These results validate the NEMD for the evaluation of permeation in FO. On the other hand, the permeation is much derived from the theoretical values when the interaction between the solvent and solute atoms is relatively large. However, the simulated permeation was consistent with the theoretical curve, correcting the solution concentration by the coordination number of the solvent atoms to the solute atoms. Our results imply that permeation flux through the FO membrane is significantly changed by the interaction between the solute and the solvent and can be theoretically predicted by calculating the coordination number of the solvent to the solute, which can be readily estimated by equilibrium molecular dynamics simulation.

Formation of a Pt-MgO Solid Solution: Analysis by X-ray Absorption Fine Structure Spectroscopy.

Thermal treatment of Pt nanoparticles or Pt(acac)2 supported on MgO resulted in the formation of a solid solution of Pt-MgO, as evidenced by Pt L3-edge X-ray absorption fine structure spectroscopy. The valence of Pt in the Pt-MgO solid solution was determined to be 4+. A characteristic shrinkage of the Pt-O bond distance was observed in comparison with that of the nearest-neighboring Mg-O bond in MgO, which agreed with the density functional theory (DFT) calculations. The segregation of Pt and MgO proceeded with a further increase in the thermal treatment temperature up to 1273 K. The dispersion of Pt on MgO measured through CO adsorption was much higher than that on Al2O3 or SiO2 owing to the formation of the Pt-MgO solid solution.

Characterization of Hydration Water Bound to Choline Phosphate-Containing Polymers.

Zwitterionic methacrylate polymers with either choline phosphate (CP) (poly(MCP)) or phosphorylcholine (PC) (poly(MPC)) side groups were analyzed to characterize the bound hydration water molecules as nonfreezing water (NFW), intermediate water (IW), or free water (FW). This characterization was carried out by differential scanning calorimetry (DSC) of polymer/water systems, and the enthalpy changes of cold crystallization and melting were determined. The electron pair orientation of CP is opposite to that of PC, and the former binds the alkyl terminal groups at the phosphate esters. The numbers of NFW and IW molecules per monomer unit of poly(MCP) with an isopropyl terminal group were estimated to be 10.7 and 11.3 mol/mol, respectively, which were slightly greater than those of the poly(MCP) bearing an ethyl terminal group. More NFW and IW molecules hydrated the phosphobetaine polyzwitterions, poly(MCP) and poly(MPC), compared with carboxybetaine and sulfobetaine polymers. Moreover, the hydration states of polyelectrolytes were compared with the zwitterionic polymers. Finally, we discuss the relationship between the amount of hydration water and bio-inert properties.

Intercalation-Induced Ordered Nanostructure in the Interlayer Modified with Methylviologen by Molecular Dynamics Simulation.

Intercalation of phenol in montmorillonite, a representative layered material, has historically been investigated, and modification of the interlayer with methylviologen (Mont-MV) results in color change due to formation of a charge-transfer complex. Its detailed nanostructure, however, has yet been revealed owing to its small gallery height and poor crystallinity. In the present study, we performed molecular dynamics simulation to investigate structural changes in Mont-MV by the intercalation of phenol. The value of the basal spacing of Mont-MV was well consistent with that reported experimentally, and the MV cations were distributed horizontally. Successive intercalation of phenol revealed that the interlayer swelled nonlinearly and both the MV cations and phenol molecules were tilted, which were roughly parallel to each other. The obtained ordered nanostructure was similar to that reported in the charge-transfer complex crystal of the MV cation and the naphthol derivative. Thus, the parallel orientation in the interlayer was found to be the key for the color reaction. Combined with the fact that the phenol molecules interacted with the Mont layers, the role of the MV cation was found to be that of a pillar for providing sufficient gallery height, and the formation of the charge-transfer complex is the secondarily derived function.

Inhomogeneity of Organically Modified Montmorillonite Revealed by Molecular Dynamics Simulation.

The modification of an interlayer of layered materials by intercalation with an organoammonium ion has been a promising method to control the polarity of the two-dimensional nanospace. Montmorillonite is one of the best-known examples, and the modification with octadecyltrimethylammonium ion (Mont-C18) results in adsorption of anthracene and pyrene together with specific excimer emission, while the nanostructure is yet to be uncovered at the molecular level because the gallery height is only ca. 27 Å. We, herein, investigated the nanostructure of this nanocomposite by molecular dynamics (MD) simulation, combined with analysis of molecular orientations against the Mont layer. The gallery height of Mont-C18 was well consistent with the experimental value, which was linearly increased along with the intercalation of anthracene. Anthracene was segregated on the Mont layer with its short and long molecular axes vertical in the early and late stages, respectively. In contrast, C18 was initially rather horizontal, forming the so-called pseudotrimolecular layer. Pushed out by anthracene, distribution and orientation of C18 were gradually changed: the third molecular layer was distinctly observed in the center of the interlayer in the early stage, and the orientation was changed to vertical in the late stage. Thus, the continuous increase in the gallery height is ascribed to soft response of C18 to the intercalation. Summarizing the abovementioned results, it was concluded that Å-order inhomogeneity is introduced in the interlayer by the intercalation of anthracene, which is significant in ideal design of the two-dimensional nanospace.

Spreading Dynamics of a Precursor Film of Ionic Liquid or Water on a Micropatterned Polyelectrolyte Brush Surface.

Time evolution of the microscopic wetting velocity of 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (EMI-TFSI) or water on a micrometer-scale line-patterned surface with a poly(3-sulfopropyl methacrylate) brush and a hydrophobic perfluoroalkyl monolayer was precisely measured by direct observation using optical microscopy and a selective dyeing method over a long period (178 days). When a liquid droplet was placed on the dyed line-patterned brush surface, the liquid penetrated and spread into the polymer brush layer, forming a precursor thin film that extended beyond the macroscopic contact line. The elongation proceeded in two stages by an adiabatic process followed by a diffusive process. The elongation distance X increased with time in proportion to t2.6 for water and t0.81 for EMI-TFSI during the adiabatic process. In a diffusive process, the advancing velocity of the precursor film was markedly reduced to be expressed as X ∝ t0.66 for water and X ∝ t0.21 for EMI-TFSI, indicating that the diffusive process was affected by the energy dissipation of the wetting system. The high viscosity and the strong molecular interaction of EMI-TFSI with the polymer brush gave a large entropy change during the wetting process to result in a slower spreading velocity.

Physicochemical compatibility of highly-concentrated solvate ionic liquids and a low-viscosity solvent.

High ionic carrier mobilities are important for the electrolyte solutions used in high-performance batteries. Based on the functional sharing concept, we fabricated mixed electrolytes consisting of solvate ionic liquids (SIL), which are highly concentrated solution electrolyte, and the non-coordinating low-viscosity dilution solvent 1,1,2,2-tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether (HFE). We investigated the thermal, transport, and static properties of electrolytes with different ratios of SIL to HFE. In particular, the interactions between the SILs and HFE and static correlations of the coordinating (ether-based molecules), non-coordinating (HFE), and carrier ionic species (lithium salt) were clarified by applying the excess density concept. Ether molecules always formed strong complexes with lithium cations regardless of the absence or presence of HFE. The repulsion force between the SILs and HFE was strongly affected by lithium salt concentration. From our results, we proposed dissociation/association models for these electrolyte systems.

Adsorption of Bovine Serum Albumin on Poly(vinylidene fluoride) Surfaces in the Presence of Ions: A Molecular Dynamics Simulation.

Adsorption of bovine serum albumin (BSA) on poly(vinylidene fluoride) (PVDF) surfaces in an aqueous environment was investigated in the presence and absence of excess ions using molecular dynamics simulations. The adsorption process involved diffusion of protein to the surface and dehydration of surface-protein interactions, followed by adsorption and denaturation. Although adsorption of BSA on PVDF surface was observed in the absence of excess ions, denaturation of BSA was not observed during the simulation (1 µs). Basic and acidic amino acids of BSA were found to be directly interacting with PVDF surface. Simulation in a 0.1 M NaCl solution showed delayed adsorption of BSA on PVDF surfaces in the presence of excess ions, with BSA not observed in close proximity to PVDF surface within 700 ns. Adsorption of Cl- on PVDF surface increased its negative charge, which repelled negatively charged BSA, thereby delaying the adsorption process. These results will be helpful for understanding membrane fouling phenomena in polymeric membranes, and fundamental advancements in these areas will lead to a new generation of membrane materials with improved antifouling properties and reduced energy demands.

Crystal and electronic structures of substituted halide perovskites based on density functional calculation and molecular dynamics.

Durability of organo-lead halide perovskite are important issue for its practical application in a solar cells. In this study, using density functional theory (DFT) and molecular dynamics, we theoretically investigated a crystal structure, electronic structure, and ionic diffusivity of the partially substituted cubic MA0.5X0.5PbI3 (MA = CH3NH3+, X = NH4+ or (NH2)2CH+ or Cs+). Our calculation results indicate that a partial substitution of MA induces a lattice distortion, resulting in preventing MA or X from the diffusion between A sites in the perovskite. DFT calculations show that electronic structures of the investigated partially substituted perovskites were similar with that of MAPbI3, while their bandgaps slightly decrease compared to that of MAPbI3. Our results mean that partial substitution in halide perovskite is effective technique to suppress diffusion of intrinsic ions and tune the band gap.

Effects of water concentration on the free volume of amino acid ionic liquids investigated by molecular dynamics simulations.

Amino acid ionic liquids (AAILs) are gaining attention because of their potential in CO2 capture technology. Molecular dynamics simulations of AAILs tetramethylammonium glycinate ([N1111][Gly]), tetrabutylammonium glycinate ([N4444][Gly]), and 1,1,1-trimethylhydrazinium glycinate ([aN111][Gly]) and their corresponding mixtures with water were performed to investigate the effect of water concentration on the cation-anion interactions. The water content significantly influenced the free volume (FV) and fractional free volume (FFV) of the AAILs that varied with the hydrophobic and hydrophilic nature of the ion pairs. Under dry conditions, the FFV increased with increasing cation molecular sizes, indicative of proportional adsorption of any inert gases, such as N2, as consistent with experimental observations. Furthermore, the polarity of the cation played an important role in FFV and hence the diffusion of the AAILs. Density functional theory calculations suggested that hydrophilic [aN111][Gly] featured stronger interactions in the presence of water, whereas the hydrophobic IL showed weaker interactions. The carboxylate group of glycinate displayed stronger interactions with water than the cation. The computational study provided qualitative insight into the role of FV of the AAILs on CO2 and N2 absorption and suggests that [aN111][Gly] has CO2 adsorption capacity in the presence of water superior to that of other studied AAILs.

Effect of Y220C mutation on p53 and its rescue mechanism: a computer chemistry approach.

Mutation causes inactivation of 'p53' tumor suppressor protein in almost fifty percent of cancers in humans. Outside the DNA-binding surface of p53, Y220C is the most common cancerous mutation. Previous studies have shown that a surface cavity is created by this mutation which destabilizes p53. PhiKan083, a carbazole derivative capable of binding with that cavity, and slows down its thermal denaturation rate. We investigated, theoretically, on mechanisms of structural stability loss due to Y220C mutation and mechanisms of stability restoration by PhiKan083 at the atomic level. From this study it is found that in Tp53C, Tyr220 has five electrostatic interactions with residues Val 147, Prol51, Pro153 and Pro223 located on S3/S4 loop and S7/S8 loop. The S7/S8 loop is stabilized by these electrostatic interactions. Due to the Y220C mutation all these electrostatic interactions are lost. As a result the structural fluctuation occurs at S7/S8 loop, and the loop is displaced from its original position after 6 ns MD simulation. When PhiKan083 is present (inserted) at the mutation site it provides five electrostatic interactions with Pro155, Glu221 and Thr230, and two hydrogen bonds with Leu145 and Asp228, respectively. These interactions provided by Pkikan083 stabilized the S7/S8 loop, and as a result it couldn't be displaced. Our results showed that due to Y220C mutation p53 became destabilized through structural fluctuations surrounding the mutation site. When PhiKan083 is present at the Y220C mutation site (in 2vuk), it provides electrostatic and hydrogen bonding interactions among residue-220, its neighboring residues and PhiKan08. These interactions give additional stability to Y220C mutant p53, thus Y220C mutant p53 doesn't destabilize.

A computational chemistry study on friction of h-MoS2. Part II. Friction anisotropy.

In this work, the friction anisotropy of hexagonal MoS(2) (a well-known lamellar compound) was theoretically investigated. A molecular dynamics method was adopted to study the dynamical friction of two-layered MoS(2) sheets at atomistic level. Rotational disorder was depicted by rotating one layer and was changed from 0° to 60°, in 5° intervals. The superimposed structures with misfit angle of 0° and 60° are commensurate, and others are incommensurate. Friction dynamics was simulated by applying an external pressure and a sliding speed to the model. During friction simulation, the incommensurate structures showed extremely low friction due to cancellation of the atomic force in the sliding direction, leading to smooth motion. On the other hand, in commensurate situations, all the atoms in the sliding part were overcoming the atoms in counterpart at the same time while the atomic forces were acted in the same direction, leading to 100 times larger friction than incommensurate situation. Thus, lubrication by MoS(2) strongly depended on its interlayer contacts in the atomic scale. According to part I of this paper [Onodera, T., et al. J. Phys. Chem. B 2009, 113, 16526-16536], interlayer sliding was source of friction reduction by MoS(2) and was originally derived by its material property (interlayer Coulombic interaction). In addition to this interlayer sliding, the rotational disorder was also important to achieve low friction state.

The effect of R249S carcinogenic and H168R-R249S suppressor mutations on p53-DNA interaction, a multi scale computational study.

In this study we have undertaken the theoretical analysis of the effect of R249S carcinogenic and H168R-R249S suppressor mutation at core domain of the tumor suppressor protein p53, on its natural interaction with DNA using a newly developed method. The results show that the carcinogenic mutation R249S affects the flexibility of L3 loop region in p53, inducing the loss of important hydrogen bonds observed at interaction in the wild-type with DNA, on the other hand the suppressor mutation H168R on the R249S assists in maintaining the wild-type like flexibility of the L3 region in p53 and thus recover the interaction terms lost in the carcinogenic mutation alone. The present study sets a new direction in the development of new drugs that may restore the interactions that lost as a consequence of the carcinogenic mutations in p53.

Quantum chemistry study on absorption spectra, electronic and electrical properties of organic dye on anatase(001).

As the most reactive surface, the stoichiometric O-bridge terminated anatase(001) surface attracted considerable attentions in many application fields. The interfacial electron transfer in dye-sensitized anatase(001) plays a principal role in a variety of photoinduced reactions. In the present work, the UV-vis absorption spectrum of TiO2 bulk and different surface models were calculated by means of tight-binding quantum chemical molecular dynamics program "Colors-excite" for the first time. The thickness dependence on electronic and electrical properties of anatase(001) surface was achieved. The anatase(001) surface with a thickness of 1.0 nm shows excellent electronic and electrical properties. Moreover, the most suitable binding mode (dissociative adsorption) and absorption spectra of perylene with acrylic acid (PAA) on the optimum anatase(001) were investigated. A significant red-shift was observed from the UV-vis absorption spectrum of PAA/anatase(001) system. The red-shift occurring when PAA adsorbed on anatase(001) surface suggests that PAA/anatase(001) may be potential candidate for dye-sensitized solar cell. This study also proposed an effective computational tool "Colors-excite" to study of the electronic excitation properties for both molecular and periodic systems.

Tribochemical reaction dynamics of molybdenum dithiocarbamate on nascent iron surface: a hybrid quantum chemical/classical molecular dynamics study.

Using a hybrid quantum chemical/classical molecular dynamics method, we have studied the tribochemical reaction dynamics of molybdenum dithiocarbamate (MoDTC), a commonly used friction modifier in automobile engine oils. MoDTC molecule adsorbed on rubbing nascent iron surface was situated. We firstly investigated the dynamic behavior of MoDTC molecule on the rubbing Fe(001) surface. During the friction simulation, the elongation of Mo-O bonds was observed, forming the Mo2S4 and thiocarbamic acid molecules. To unveil the detailed mechanism of this bond elongation, the electronic states of the MoDTC molecule and Fe(001) surface were computed, and the catalytic effects of Fe(001) surface to the molecule was found. We also found that extreme friction would influence the complete Mo-O bond dissociation. By using the hybrid quantum chemical/classical molecular dynamics method, we successfully simulated the tribochemical reaction dynamics of MoDTC as a friction modifier and obtained the influences of nascent iron surface and friction on its chemical reaction.

A computational chemistry study on friction of h-MoS(2). Part I. Mechanism of single sheet lubrication.

In this work, we theoretically investigated the friction mechanism of hexagonal MoS(2) (a well-known lamellar compound) using a computational chemistry method. First, we determined several parameters for molecular dynamics simulations via accurate quantum chemistry calculations and MoS(2) and MoS(2-x)O(x) structures were successfully reproduced. We also show that the simulated Raman spectrum and peak shift on X-ray diffraction patterns were in good agreement with those of experiment. The atomic interactions between MoS(2) sheets were studied by using a hybrid quantum chemical/classical molecular dynamics method. We found that the predominant interaction between two sulfur layers in different MoS(2) sheets was Coulombic repulsion, which directly affects the MoS(2) lubrication. MoS(2) sheets adsorbed on a nascent iron substrate reduced friction further due to much larger Coulombic repulsive interactions. Friction for the oxygen-containing MoS(2) sheets was influenced by not only the Coulomb repulsive interaction but also the atomic-scale roughness of the MoS(2)/MoS(2) sliding interface.