Molecular Dynamics Simulation of Platinum Particles Between Graphite Walls

Abstract

We report preliminary molecular dynamics simulations results for platinum atoms confined between two parallel graphite surfaces. The system shows phase transition characteristics corresponding to a second order transition. Significant structural changes are also observed in the range of temperature studied. We have also investigated the effects of two dfferent Pt-wall interaction potentials: the 9-3 form suggested by Crowell and the 10-4 form originally proposed by Steele. The results show that the two systems have rather different structural characteristics but similar thermodynamic behavior.     

Density functional theory for the selective adsorption of small molecules on a surface modified with polymer brushes

A density functional method based on weighted density approximation is extended to study the selective adsorption of small molecules on a surface modified with end-grafted square-well chains. The excess part of the Helmholtz free energy functional is divided into two components: the hard sphere repulsion and the square-well attraction. The equation of state for hard sphere chain fluids developed by Liu et al. is used to calculate the repulsive part of the excess Helmholtz free energy functional, and the equation of state for square-well chain fluid with variable range developed by Li et al. is employed to calculate the attractive part. With this theoretical model, we examine the physical properties of the grafted polymer and the selective adsorption of small molecules on the modified surface.     

Adsorption of phenol and aniline on natural and organically modified montmorillonite: experiment and molecular modelling

Natural and intercalated Wyoming montmorillonite (MMT) with the tetramethylammonium (TMA) cations were used for the adsorption of phenol and aniline. Laboratory experiments characterised by adsorption isotherms were compared with the results of molecular modelling simulations. Aniline adsorbed itself strongly on MMT; while using the TMA intercalates (TMA-MMT), its adsorption decreased. On the contrary, the adsorption of phenol on TMA-MMT was moderately higher than on the MMT surface. The MMT surface models were described by empirical force field used in molecular mechanics and dynamics. The Burchart–Universal force field was used in the Cerius² modelling environment. The modelling results revealed the important role of water forming a moderately concentrated layer on the pure MMT surface. Water molecules enable the adsorption of aniline on MMT and, on the contrary, repel phenol molecules from MMT. In the case of TMA-MMT, lower amount of water near a silicate layer caused decrease in the aniline adsorption and, on the contrary, increase in the phenol adsorption.     

Smart Monte Carlo Algorithm for the Adsorption of Molecules at a Surface

Abstract

A modified grand canonical ensemble Monte Carlo (GCMC) technique has been developed to simulate adsorption isotherms for molecules on or near a surface. The speed and accuracy of the simulation is increased by using a non-uniform distribution function, related to the force field exerted by the surface and the current configuration, to generate coordinates for the creation of new particles in the simulation. With this method, isotherms are generated more efficiently than with current techniques in which the creation step relies on a uniform distribution to generate the coordinates of a new molecule. This is shown by comparing the calculation of an isotherm for a simple molecule adsorbed on a graphite substrate from a traditional GCMC simulation with that calculated using this new technique.     

Behavior of Aromatic Molecules in Silicalite by the Direct Integration of the Configurational Integral

Abstract

Adsorption data of aromatic molecules adsorbed in silicalite show highly unusual characteristics which were attributed to structural effects caused by the comparable size of molecules and pores. In this study, the interaction of aromatic compounds with silicalite are examined on the molecular level. The interactions are calculated by atom-atom approximation using Lennard-Jones potentials. The constants are calculated, without fitting, from Kirkwood-Muller formulas. Benzene and p-xylene are represented as a rigid structure of 12 and 18 atom centers. The model is anisotropic.

The diffusional behavior of molecules is examined by minimizing the potential energy in the channels which requires less computational time than Molecular Dynamics. The activation energy for the diffusion of benzene, 27.6 kJ/mol, is in excellent agreement with data, 28.8 kJ/mol. The results indicate that both molecules can enter the smaller zig-zag channels. The energetically most favorable location in the main channels is the mid-point between intersections. All rotations are restricted in the channels but the molecules can rotate in any direction (with some movement of the center) at intersections.

The Henry's law constant and internal energy of adsorption at zero coverage are calculated by direct integration of the configurational integral. Direct integration is more efficient than Monte Carlo and Molecular Dynamics simulations since the molecules are highly restricted in the pores. The predicted internal energy of adsorption, ? 54.86 and ? 75.30 kJ/mol for benzene and p-xylene is in good agreement with data of ? 50.92 and ? 62.15 kJ/mol respectively. There is appreciable difference between the predicted and experimental Henry's law constants. The agreement can be improved by fitting the Lennard-Jones constants which has not been attempted.

Although the calculations are performed at infinite dilution and entropy effects are not included, the results bring insight to the behavior of molecules in highly restricted environments such as in tight pores. Similar simplified calculations can be used to close the gap between highly idealized molecular simulations and complicated systems common in real applications.     

Protein adsorption and displacement at lipid layers determined by total internal reflection fluorescence (TIRF)

In many drug delivery systems such as liposomes, the adsorption of interstitial proteins upon administration can have a huge effect on the elimination, release, and stability of the delivery system. For example, it is assumed that PEGylated liposomes prevent the adsorption of opsonins and thereby prolong the circulation time in vivo, and EMEA guidelines recommend that more than 80% of the protein antigen is adsorbed in the formulation of adjuvant systems. However, few methods exist to elucidate this protein adsorption. The present study indicates that total internal reflection fluorescence (TIRF) is a possible method to examine the adsorption and exchange of proteins at lipid surfaces. In the TIRF set-up, a lipid layer can be formed [exemplified with dimethyldioctadecylammonium bromide (DDA) and D-(+)-trehalose 6,6’-dibehenate (TDB)] whereafter protein (i.e., ovalbumin or an antigen, Ag85B-ESAT-6) is adsorbed, and these proteins can subsequently be displaced by the abundant interstitial protein (i.e., serum albumin).     

Separation of Nadolol Stereoisomers by Chiral Liquid Chromatography at Analytical and Preparative Scales

The separation of the four nadolol stereoisomers on Chiralpak® AD by chiral liquid chromatography was carried out at both analytical and preparative scales. A screening of possible mobile‐phase compositions was performed using different alcohol–hydrocarbon mixtures. The results obtained confirm the use of 20:80:0.3 ethanol‐hexane‐diethylamine reported by McCarthy (1994) but introduce other possibilities for the complete resolution of the four nadolol stereoisomers at analytical scale, namely, the mixtures 30–40:70–60:0.3 ethanol‐heptane‐diethylamine. Additionally, this work describes how retention and resolution depend on the ethanol content in hexane and heptane mixtures. The separation of nadolol stereoisomers is also carried out at preparative scale and different alcohol–hydrocarbon compositions are proposed, depending on the target component to be obtained. Particularly, this work presents the experimental separation of the more retained nadolol stereoisomer (RSR‐nadolol) by simulated moving bed (SMB) chromatography using an 80:20:0.3 ethanol‐heptane‐diethylamine mobile phase. For a 2 g/l feed concentration, RSR‐nadolol is 100% recovered at the extract outlet stream, 100% pure, and with a system productivity of 0.65 g_{RSR‐nadolol}/(l_bed^.h) and a solvent consumption of 9.6 l_solvent/g_{RSR‐nadolol}. Chirality 25:197–205, 2013. © 2013 Wiley Periodicals, Inc.     

Chemistry of Heliangine

Novel three-proton signals at δ3.6~2.0 in the 60 and 100Mc NMR spectra of helianginone (II) were interpreted by several analytical methods. These protons were concluded to form an isolated ABC system which contains two chemical shifts, δ_AC= 100.2 and δ_BC= 81.6 cps, and three coupling constants, J_AB=4.9, J_BC= 10.2 and J_CA= -14.8 cps. In this system it is very significant that J_CA is negative. These protons were assigned as in the partial structure (a) of II.     

Synthetic Studies on Carbohydrate Antibiotics

Methyl N, N′-diacetyl-α-kasugaminide and its C₄ epimer were synthesized starting from d-glucose, and their configurations were discussed.     

Fate of pathological prion (PrPsc92–138) in soil and water: prion-clay nanoparticle molecular dynamics

Pathogenic prion protein scrapie (PrP^sc) may contaminate soils for decades and remain in water in colloidal suspension, providing infection pathways for animals through the inhalation of ingested dust and soil particles, and drinking water. We used molecular dynamics simulations to understand the strong binding mechanism of this pathogenic peptide with clay mineral surfaces and compared our results to experimental works. We restricted our model to the moiety PrP(92–138), which is a portion of the whole PrP^sc molecule responsible for infectivity and modeled it using explicit solvating water molecules in contact with a pyrophyllite cleavage plane. Pyrophyllite is taken as a model for common soil clay, but it has no permanent structural charge. However, partial residual negative charges occur on the cleavage plane slab surface due to a slab charge unbalance. The charge is isotropic in 2D and it was balanced with K⁺ ions. After partially removing potassium ions, the peptide anchors to the clay surface via up to 10 hydrogen bonds, between protonated lysine or histidine residues and the oxygen atoms of the siloxane cavities. Our results provide insight to the mechanism responsible for the strong association between the PrP^sc peptide and clay nanoparticles and the associations present in contaminated soil and water which may lead to the infection of animals.