Molecular dynamics simulation of liquid sulfur dioxide

A previously proposed model for molecular dynamics (MD) simulation of liquid sulfur dioxide, SO(2), has been reviewed. Thermodynamic, structural, and dynamical properties were calculated for a large range of thermodynamic states. Predicted (P,V,T) of simulated system agrees with an elaborated equation of state recently proposed for liquid SO(2). Calculated heat capacity, expansion coefficient, and isothermal compressibility are also in good agreement with experimental data. Calculated equilibrium structure agrees with X-ray and neutron scattering measurements on liquid SO(2). The model also predicts the same (SO(2))(2) dimer structure as previously determined by ab initio calculations. Detailed analysis of equilibrium structure of liquid SO(2) is provided, indicating that, despite the rather large dipole moment of the SO(2) molecule, the structure is mainly determined by the Lennard-Jones interactions. Both single-particle and collective dynamics are investigated. Temperature dependency of dynamical properties is given. The MD results are compared with previous findings obtained from the analysis of inelastic neutron scattering spectra of liquid SO(2), including wave-vector dependent structural relaxation, tau(k), and viscosity, eta(k).     

Molecular dynamics simulation of nanoparticle self-assembly at a liquid-liquid interface

We have used molecular dynamics simulations to investigate the in situ self-assembly of modified hydrocarbon nanoparticles (mean diameter of 1.2 nm) at a water-trichloroethylene (TCE) interface. The nanoparticles were first distributed randomly in the water phase. The MD simulation shows the in situ formation of nanoparticle clusters and the migration of both single particles and clusters from the water phase to the trichloroethylene phase, possibly due to the hydrophobic nature of the nanoparticles. Eventually, the single nanoparticles or clusters equilibrate at the water-TCE interface, and the surrounding liquid molecules pack randomly when in contact with the nanoparticle surfaces. In addition, the simulations show that the water-TCE interfacial thickness analyzed from density profiles is influenced by the presence of nanoparticles either near or in contact with the interface but is independent of the number of nanoparticles present. The nanoparticles, water molecules, and TCE molecules all exhibit diffusion anisotropy.     

Molecular dynamics simulation of the cybotactic region in gas-expanded methanol-carbon dioxide and acetone-carbon dioxide mixtures

Local solvation and transport effects in gas-expanded liquids (GXLs) are reported based on molecular simulation. GXLs were found to exhibit local density enhancements similar to those seen in supercritical fluids, although less dramatic. This approach was used as an alternative to a multiphase atomistic model for these mixtures by utilizing experimental results to describe the necessary fixed conditions for a locally (quasi-) stable molecular dynamics model of the (single) GXL phase. The local anisotropic pair correlation function, orientational correlation functions, and diffusion rates are reported for two systems: CO2-expanded methanol and CO2-expanded acetone at 298 K and pressures up to 6 MPa.     

Molecular dynamics simulation of dense carbon dioxide fluid on amorphous silica surfaces

Molecular dynamics (MD) simulations of dense carbon dioxide on the amorphous dehydroxylated silica surfaces have been carried out. The adsorption potential surfaces of the silica solids have been obtained in order to evaluate the characteristics of the amorphous surfaces. The atom density profiles, adsorption free energy profiles, surface orientation order parameters, and radial distribution functions for the CO2 molecules have been presented in order to study the effect of the amorphous surfaces on the microscopic interfacial structure properties of the CO2 molecules. The translational diffusion and orientation rotation at silica surfaces have also been investigated. It was observed that there is marked hindrance of the translational diffusion and orientation rotation of CO2 molecules near amorphous silica surfaces.     

Molecular dynamics simulation of premelting and melting phase transitions in stoichiometric uranium dioxide

Results of molecular dynamics (MD) simulation of UO2 in a wide temperature range are presented and discussed. A new approach to the calibration of a partly ionic Busing-Ida-type model is proposed. A potential parameter set is obtained reproducing the experimental density of solid UO2 in a wide range of temperatures. A conventional simulation of the high-temperature stoichiometric UO2 on large MD cells, based on a novel fast method of computation of Coulomb forces, reveals characteristic features of a premelting lambda transition at a temperature near to that experimentally observed (T(lambda)=2670 K). A strong deviation from the Arrhenius behavior of the oxygen self-diffusion coefficient was found in the vicinity of the transition point. Predictions for liquid UO2, based on the same potential parameter set, are in good agreement with existing experimental data and theoretical calculations.     

Molecular dynamics simulation of DNA‐directed assembly of nanoparticle superlattices using patterned templates

DNA‐directed assembly is a well developed approach in constructing desired nano‐architectures. On the other hand, E‐beam lithography is widely utilized for high resolution nano‐scale patterning. Recently, a new technique combining these two methods was developed to epitaxially grow DNA‐mediated nanoparticle superlattices on patterned substrates. However, defects are observed in epitaxial layers which restricts this technique from building large‐scale superlattices for real applications. Here we use molecular dynamics simulations to study and predict defect formation on adsorbed superlattice monolayers. We demonstrate that this epitaxial growth is energetically driven by maximizing DNA hybridization between the epitaxial layer and the substrate and that the shape anisotropy of the DNA‐mediated template posts leads to structural defects. We also develop design rules to dramatically reduce defects on epitaxial layers. Ultimately, with the assist of the computational study, this technique will open the door to constructing well‐ordered, three‐dimensional novel nanomaterials. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 1687–1692     

Characterization of titanium dioxide nanoparticles using molecular dynamics simulations

Molecular dynamics simulations of titanium dioxide nanoparticles in the three commonly occurring phases (anatase, brookite, and rutile) are reported. The structural properties inferred by simulated X-ray diffraction patterns of the nanoparticles were investigated. The titanium-oxygen bond length as a function of size, phase, and temperature was determined and was found to be dependent on the coordination environment of the titanium and independent of phase and size. The equilibrium Ti-O bond length is 1.86 A for a four-coordinated titanium ion, 1.92 A for a five-coordinated titanium ion, and 1.94 A for an octahedral titanium ion. Smaller nanoparticles are characterized by a higher fraction of titanium ions that are four and five coordinated, due to the larger surface area-to-volume ratios. The surface energies for anatase, rutile, and brookite particles were reported. The surface energy of the nanoparticle increases and approaches a constant value as the particle gets bigger. The surface energies of small rutile particles are higher than that for anatase particles of a similar size, consistent with anatase being the more stable phase of nanocrystalline titanium dioxide.     

Systematic coarse-graining of nanoparticle interactions in molecular dynamics simulation

A recently developed multiscale coarse-graining procedure [Izvekov, S.; Voth, G. A. J. Phys. Chem. B 2005, 109, 2469] is extended to derive coarse-grained models for nanoparticles. The methodology is applied to C(60) and to carbonaceous nanoparticles produced in combustion environments. The coarse-graining of the interparticle force field is accomplished applying a force-matching procedure to data obtained from trajectories and forces from all-atom MD simulations. The CG models are shown to reproduce accurately the structural properties of the nanoparticle systems studied, while allowing for MD simulations of much larger self-assembled nanoparticle systems.     

Self-assembly of a tripodal pseudorotaxane on the surface of a titanium dioxide nanoparticle

This paper describes the self-assembly of a heterosupramolecular system consisting of a tripodal viologen, adsorbed at the surface of a titanium dioxide nanoparticle, that threads a crown ether to form a pseudorotaxane. The viologen, a 1,1'-disubstituted-4,4'-bipyridinium salt with a rigid tripodal anchor group, has been synthesized. This viologen is adsorbed at the surface of a titanium dioxide nanoparticle in solution. As intended, this tripodal viologen is both oriented normal to and displaced from the surface of the nanoparticle and threads a crown ether to form the heterosupramolecular complex. The threading of the crown ether by the tripodal viologen to form the above pseudorotaxane complex at the surface of a titanium dioxide nanoparticle has been studied by (1)H NMR, optical absorption spectroscopy, and cyclic voltammetry.     

Molecular-dynamics simulation of nanoclusters of crystal modifications of titanium dioxide

The thermodynamic and structural properties of titanium dioxide nanoclusters belonging to the two most common crystal modifications, rutile and antase, were studied by molecular-dynamics simulation. The local densities of particles in the systems, two-particle distribution functions, and electric potential profiles were calculated. The influence of the size of nanoclusters on their properties and structure was examined.     

Molecular dynamics simulation of liquid trimethylphosphine

Structural and dynamical properties of liquid trimethylphosphine (TMP), (CH(3))(3)P, as a function of temperature is investigated by molecular dynamics (MD) simulations. The force field used in the MD simulations, which has been proposed from molecular mechanics and quantum chemistry calculations, is able to reproduce the experimental density of liquid TMP at room temperature. Equilibrium structure is investigated by the usual radial distribution function, g(r), and also in the reciprocal space by the static structure factor, S(k). On the basis of center of mass distances, liquid TMP behaves like a simple liquid of almost spherical particles, but orientational correlation due to dipole-dipole interactions is revealed at short-range distances. Single particle and collective dynamics are investigated by several time correlation functions. At high temperatures, diffusion and reorientation occur at the same time range as relaxation of the liquid structure. Decoupling of these dynamic properties starts below ca. 220 K, when rattling dynamics of a given TMP molecules due to the cage effect of neighbouring molecules becomes important.     

Molecular dynamics simulation of semirigid polymers

The chain rigidity of poly(p-hydroxybenzoate) was estimated through the theoretical evaluation of its persistence length (L_p). A non-Brownian molecular dynamics (MD) simulation of an isolated chain with 20 monomeric units was performed. The sampled conformational population was analyzed and the orientational correlation function between monomeric units along the chain was calculated. An algorithm based on the worm-like chain model was applied to evaluate the persistence length. The results were compared with those obtained from equilibrium models like the freely-rotating-chain and the rotational-matrix method with fluctuations. Equilibrium models give different results depending on the degree of accuracy used in describing the monomeric unit. The inclusion of thermal fluctuations is crucial to obtain realistic results. These coincide with those given by MD simulation when only nearest-neighbour orientational correlations are taken into account: inclusion of higher-order correlation terms leads to lower values of the persistence length. The origin of this discrepancy was investigated. The MD simulation results are characterized by an overrepresentation of conformations with a short end-to-end distance resulting from an anomalous energy concentration in the first bending mode of the chain. In analogy with previous simulation results from systems characterized by a week coupling amoung their degrees of freedom, failure in the energy equipartition is proposed as a likely explanation of the anomalous dynamical behaviour.     

液态水的分子动力学模拟

用分子动力学(MD)模拟方法在150~376K的温度范围内对液态水的微正则系统进行了研究。考察了液态水的结构及其性质。模拟采用了由从头算得出的柔性水-水相互作用势MCYL。对时间和空间的平均得出了液态中水分子几何构型及温度改变所引起的液态水结构变化。对径向分布函数gOH, gOO, gHH及配位数的分析表明, 在所考察的温度范围内, 每个水分子与相邻分子形成的氢键数为2~3, 水分子在参与的2个氢键中同时作为授受体。结合对振动谱的研究表明在低温时液态水形成的网络结构可能随温度的升高而形成小的簇结构。     

Molecular dynamics simulation of the structure of mixed ligand shells stabilizing cadmium selenide nanoparticle surfaces with different curvatures

A full-atomic molecular dynamics simulation has been performed for a ligand shell of colloidal cadmium selenide quantum dots. Trioctylphosphine, trioctylphosphine oxide, octadecylphosphonic acid, and hexadecylamine have been used as ligands. For a mixture of the two former ligands, the effect of surface curvature on the fraction of surface ions of quantum dots bonded to ligands has been studied. It has been shown that, for particles with radii of 1.9 and 4.5 nm, every second and approximately third cadmium atom, respectively, is bonded to trioctylphosphine oxide. Partial introduction of octadecylphosphonic acid and hexadecylamine may increase the fraction of bonded surface atoms by more than two times.     

Molecular dynamics study of carbon dioxide hydrate dissociation

We present results from a molecular dynamics study of the dissociation behavior of carbon dioxide (CO(2)) hydrates. We explore the effects of hydrate occupancy and temperature on the rate of hydrate dissociation. We quantify the rate of dissociation by tracking CO(2) release into the liquid water phase as well as the velocity of the hydrate-liquid water interface. Our results show that the rate of dissociation is dependent on the fractional occupancy of each cage type and cannot be described simply in terms of overall hydrate occupancy. Specifically, we find that hydrates with similar overall occupancy differ in their dissociation behavior depending on whether the small or large cages are empty. In addition, individual cages behave differently depending on their surrounding environment. For the same overall occupancy, filled small and large cages dissociate faster in the presence of empty large cages than when empty small cages are present. Therefore, hydrate dissociation is a collective phenomenon that cannot be described by focusing solely on individual cage behavior.     

Assembly of an electronically switchable rotaxane on the surface of a titanium dioxide nanoparticle

This paper describes the self-assembly of a heterosupramolecular system consisting of a tripodal [2]rotaxane adsorbed at the surface of a titanium dioxide nanoparticle. The tripodal [2]rotaxane consists of a dumbbell-shaped molecule, incorporating two electron-poor viologens, threading an electron-rich crown ether. The [2]rotaxane also incorporates a bulky tripodal linker group at one end and a bulky stopper group at the other end. The [2]rotaxane is adsorbed, via the tripodal linker group, at the surface of a titanium dioxide nanoparticle. The structure and function of the resulting hetero[2]rotaxane have been studied in detail by (1)H NMR spectroscopy and cyclic voltammetry. A key finding is that it is possible to electronically address and switch the above hetero[2]rotaxane.     

Development of a titanium dioxide nanoparticle pipette-tip for the selective enrichment of phosphorylated peptides

The selective enrichment of specific proteins or peptides on micropipette tips prior to mass spectrometry analysis, which can minimize non-specific interferences as well as sample loss, has been an important issue in current proteomics field. In this paper, we have developed an easy-to-use phosphopeptide-selective pipette tip in which titanium dioxide nanoparticles were embedded in monolithic structure photopolymerized from ethylene glycol dimethacrylate. The simple and convenient fabrication was feasible in a commercial polypropylene pipette tip. Phosphorylated peptides were isolated from non-phosphopeptides by TiO(2) nanoparticle and eluted by 100 mM ammonium phosphate (pH 8.5), which was compatible with 2,5-dihydroxybenzoic acid (DHB)/1% phosphoric acid matrix and allowed for direct analysis of the elution fraction by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) without the necessity of desalting pretreatment. Tryptic digested alpha-casein and beta-casein spiked into bovine serum albumin (BSA) nonphosphorylated peptides (molar ratio 1:1:10) were used to assess the selectivity of TiO(2) tips. The effect of 50 mM ammonium hydrogencarbonate, pH 8 in 50% acetonitrile used as a wash buffer in reduction of nonspecific bound peptide to TiO(2) tip was dramatic. Almost all non-phosphopeptides were not detected by MALDI-MS analysis. The lowest detectable amount of phosphopeptide was estimated at low femtomole level. The easy-to-use TiO(2)-embeded tips operated in combination with the modified wash and elution conditions enable an efficient phosphopeptide enrichment for mass spectrometric analysis.     

Electrochemical application of titanium dioxide nanoparticle/gold nanoparticle/multiwalled carbon nanotube nanocomposites for nonenzymatic detection of ascorbic acid

Titanium dioxide nanoparticle/gold nanoparticle/carbon nanotube (TiO₂/Au/CNT) nanocomposites were synthesized, and then characterized using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and energy dispersive X-ray spectroscopy (EDX). A TiO₂/Au/CNT nanocomposite-modified glassy carbon (GC) electrode was prepared using the drop coating method and was investigated using electrochemical impedance spectroscopy (EIS), cyclic voltammetry (CV), differential pulse voltammetry (DPV), and amperometric current–time response (I-T). The modified material is redox-active. The nonenzymatically detected amount of ascorbic acid (AA) on the TiO₂/Au/CNT electrode showed a linear relationship with the AA concentration, for concentrations from 0.01 to 0.08 μM; the sensitivity was 117,776.36 μA?·?cm^?2?·?(mM)^?1, and the detection limit was 0.01 μM (S/N?=?3). The results indicated that the TiO₂/Au/CNT nanocomposite-modified GC electrode exhibited high electrocatalytic activity toward AA. This paper describes materials consisting of a network of TiO₂, Au, and MWCNTs, and the investigation of their synergistic effects in the detection of AA.     

Molecular dynamics simulation of water-based nanofluids viscosity

Journal of Thermal Analysis and Calorimetry - The shear viscosity coefficients of water and water-based nanofluids with copper particles are calculated by the molecular dynamics method. Copper...     

Molecular dynamics simulation of cellulose-coated oil-in-water emulsions

The behaviors of cellulose chains and cellulose mini-crystal in oil-in-water emulsions were studied by molecular dynamics simulations to investigate the coating states and the structural features of cellulose in these emulsions. In oil-in-water emulsion, dispersed cellulose chains gradually assemble during the progress of the simulation, eventually surrounding the octane droplet. In case of a cellulose mini-crystal, the cellulose chain at the corner of the crystal first contacts with the octane droplet through its hydrophobic surface. The other cellulose chains along the crystal plane then gradually move toward the octane molecules. In both emulsions, the cellulose was found to interact with both water and octane surfaces with specific conformations that allow the CH groups of the glucose rings to contact with octane molecules, while the OH groups of these rings contact with water molecules to form hydrogen bonds. The cellulose chains on the octane droplet also contact with each other through lateral hydrogen bonding between chains. These interactions stabilize the emulsion formed by cellulose molecules as surfactants.