Structural and dynamic properties of (SiO2)6 silica nanostructures: a quantum molecular dynamics study

Structural and dynamic properties of the building block of silica nanowires, (SiO2)6, are investigated by Born-Oppenheimer quantum molecular dynamics simulations. Thirteen conformers have been identified, seven of which have not been reported before. The energy component analysis shows that the lower electrostatic interaction differentiates the global minimum from the other structures. We also observe that the maximum hardness principle can be employed to justify the molecular stability for this system. Time profiles of a few density functional reactivity indices exhibit correlations of dynamic fluctuations between HOMO and LUMO and between chemical potential and hardness. Electrophilicity, nucleaofugality, and electrofugality indices are found to change concurrently and significantly, indicating that the nanostructures sampled during the dynamic process are exceedingly reactive and rich in chemistry.     

Transport properties of acetone aqueous solutions: molecular dynamics simulation and NMR studies

Two quantities η_rel and are applied to study the nonideal acetone–water association mixture. An all-atom acetone model and a TIP5P water model have been adopted for molecular dynamics simulation. We study the transport properties of the system comparing the 's of strong hydrogen bond and weak contact based on transport properties, MD simulations together with NMR experimental data and find good agreement of concentration dependence, which exhibits the cooperation effect.     

The mixed alkali effect in ionically conducting glasses revisited: a study by molecular dynamics simulation

When more than two kinds of mobile ions are mixed in ionic conducting glasses and crystals, there is a non-linear decrease of the transport coefficients of either type of ion. This phenomenon is known as the mixed mobile ion effect or Mixed Alkali Effect (MAE), and remains an unsolved problem. We use molecular dynamics simulation to study the complex ion dynamics in ionically conducting glasses including the MAE. In the mixed alkali lithium-potassium silicate glasses and related systems, a distinct part of the van Hove functions reveals that jumps from one kind of site to another are suppressed. Although, consensus for the existence of preferential jump paths for each kind of mobile ions seems to have been reached amongst researchers, the role of network formers and the number of unoccupied ion sites remain controversial in explaining the MAE. In principle, these factors when incorporated into a theory can generate the MAE, but in reality they are not essential for a viable explanation of the ion dynamics and the MAE. Instead, dynamical heterogeneity and "cooperativity blockage" originating from ion-ion interaction and correlation are fundamental for the observed ion dynamics and the MAE. Suppression of long range motion with increased back-correlated motions is shown to be a cause of the large decrease of the diffusivity especially in dilute foreign alkali regions. Support for our conclusion also comes from the fact that these features of ion dynamics are common to other ionic conductors, which have no glassy networks, and yet they all exhibit the MAE.     

Structural properties of polystyrene oligomers in different environments: a molecular dynamics study

We have performed detailed molecular dynamics simulations to investigate the effects of solvation and confinement on the structure of polystyrene (PS) oligomers in four different environments, melt, concentrated solution, dilute solution and confined concentrated solution at 450 K and 1 bar, respectively. Local packing of the monomers and the solvent (toluene, good solvent) molecules were monitored by means of radial distribution functions (RDFs). We have also investigated bond, angle, and dihedral angle distributions of the monomers. End-to-end distances, radii of gyration and persistence lengths were calculated to characterize the static properties. The chain in the dilute solution was found to exhibit more stretched conformations. Dilution effect of the solvent was observed in the RDFs between the monomer centers. Only slight conformational changes in the polymers were observed by solvation. The effect of confinement was mainly seen in the density profiles, which showed an oscillatory behavior in the confined system.     

Structural and dynamical properties of water dimer and tetramer: molecular dynamics study

A detailed evaluation of the structural and dynamical properties of isolated water dimers and tetramers using the Lemberg, Stillinger and Rahman potential energy surface and microcanonical molecular dynamics simulations are reported. The lowest-energy configurations of these clusters were obtained by simulated thermal quenching. Relative root-mean-square bond length fluctuations were used to characterize phase transitions. Solid-like, pre-melting, liquid-like, and dissociated states were identified. Global-local minimum transitions and the minimum energy path to dissociation of the dimer were also characterized.     

Electron binding energies of aqueous alkali and halide ions: EUV photoelectron spectroscopy of liquid solutions and combined ab initio and molecular dynamics calculations

Photoelectron spectroscopy combined with the liquid microjet technique enables the direct probing of the electronic structure of aqueous solutions. We report measured and calculated lowest vertical electron binding energies of aqueous alkali cations and halide anions. In some cases, ejection from deeper electronic levels of the solute could be observed. Electron binding energies of a given aqueous ion are found to be independent of the counterion and the salt concentration. The experimental results are complemented by ab initio calculations, at the MP2 and CCSD(T) level, of the ionization energies of these prototype ions in the aqueous phase. The solvent effect was accounted for in the electronic structure calculations in two ways. An explicit inclusion of discrete water molecules using a set of snapshots from an equilibrium classical molecular dynamics simulations and a fractional charge representation of solvent molecules give good results for halide ions. The electron binding energies of alkali cations computed with this approach tend to be overestimated. On the other hand, the polarizable continuum model, which strictly provides adiabatic binding energies, performs well for the alkali cations but fails for the halides. Photon energies in the experiment were in the EUV region (typically 100 eV) for which the technique is probing the top layers of the liquid sample. Hence, the reported energies of aqueous ions are closely connected with both structures and chemical reactivity at the liquid interface, for example, in atmospheric aerosol particles, as well as fundamental bulk solvation properties.     

Thermophoresis in liquids: a molecular dynamics simulation study

Thermophoresis in liquids is studied by molecular dynamics simulation (MD). A theory is developed that divides the problem in the way consistent with the characteristic scales. MD is then conducted to obtain the solution of each problem, which is to be all combined for macroscopic predictions. It is shown that when the temperature gradient is applied to the nonconducting liquid bath that contains neutral particles, there occurs a pressure gradient tangential to the particle surface at the particle-liquid interface. This may induce the flow in the interfacial region and eventually the particle to move. This applies to the material system that interacts through van der Waals forces and may be a general source of the thermophoresis phenomenon in liquids. The particle velocity is linearly proportional to the temperature gradient. And, in a large part of the given temperature range, the particle motion is in the direction toward the cold end and decreases with respect to the temperature. It is also shown that the particle velocity decreases or even reverses its sign in the lowest limit of the temperature range or with a particle of relatively weak molecular interactions with the liquid. The characteristics of the phenomenon are analyzed in molecular details.     

Local density augmentation and dynamic properties of hydrogen-and non-hydrogen-bonded supercritical fluids: a molecular dynamics study

The local density inhomogeneities in neat supercritical fluids were investigated via canonical molecular dynamics simulations. The selected systems under investigation were the polar and hydrogen-bonded fluid methanol as well as the quadrupolar non-hydrogen-bonded carbon dioxide one. Effective local densities, local density augmentation, and enhancement factors were calculated at state points along an isotherm close to the critical temperature of each system (T(r)=1.03). The results obtained reveal strong influence of the polarity and hydrogen bonding upon the intensity of the local density augmentation. It is found that this effect is sufficiently larger in the case of the polar and associated methanol in comparison to those predicted for carbon dioxide. For both fluids the local density augmentation values are maximized in the bulk density region near 0.7rho(c), a result that is in agreement with experiment. In addition, the local density dynamics of each fluid were investigated in terms of the appropriate time correlation functions. The behavior of these functions reveals that the bulk density dependence of the local density reorganization times is very sensitive to the specific intermolecular interactions and to the size of the local region. Also, the estimated local density reorganization time as a function of bulk density of each fluid was further analyzed and successfully related to two different time-scale relaxation mechanisms. Finally, the results obtained indicate a possible relationship between the single-molecule reorientational dynamics and the local density reorganization ones.     

Structural and dynamical properties of the Hg2+ aqua ion: a molecular dynamics study

Molecular dynamics simulations of the Hg2+ ion in aqueous solution have been carried out using an effective two-body potential derived from quantum mechanical calculations. A stable heptacoordinated structure of the Hg2+ first hydration shell has been observed and confirmed by extended X-ray absorption fine structure (EXAFS) experimental data. The structural properties of the Hg2+ hydration shells have been investigated using radial and angular distribution functions, while the dynamical behavior has been discussed in terms of reorientational correlation functions, mean residence times of water molecules in the first and second hydration shells, and self-diffusion coefficients. The effect of water-water interactions on the Hg2+ hydration properties has been evaluated using the SPC/E and TIP5P water models.     

Dispersing carbon nanotubes in aqueous solutions by a silicon surfactant: Experimental and molecular dynamics simulation study

The dispersion effect of carbon nanotubes (CNTs) in aqueous solutions by a silicon surfactant (ethoxy modified trisiloxane, named Ag-64) was investigated in detail using experimental method and molecular dynamics simulation. The Si–O–Si chain of silicon surfactant was flexible due to long Si–C bond and it could easily wrap onto the surface of CNTs through hydrophobic and other intermolecular interactions. The hydrophilic part of PEO provided the CNTs dispersed in the aqueous solution and prevented CNTs from aggregating in water through steric stabilization. It was found that Ag-64 could disperse CNTs with different diameters and it was an effective dispersing agent. The results of molecular dynamics simulation indicated that Ag-64 molecules could wrap onto the surface of CNTs leading to steric stabilization so that it could well disperse CNTs, and Van der Waals attraction was the dominating force of Ag-64 adsorbing onto CNTs. Our study may provide experimental and theoretical basis for using silicon surfactants to disperse CNTs, which can open the avenue of new applications for silicon surfactants.     

Understanding the pH-dependent behavior of graphene oxide aqueous solutions: a comparative experimental and molecular dynamics simulation study

Understanding the pH-dependent behavior of graphene oxide (GO) aqueous solutions is important to the production of assembled GO or reduced GO films for electronic, optical, and biological applications. We have carried out a comparative experimental and molecular dynamics (MD) simulation study to uncover the mechanisms behind the aggregation and the surface activity of GO at different pH values. At low pH, the carboxyl groups are protonated such that the GO sheets become less hydrophilic and form aggregates. MD simulations further suggest that the aggregates exhibit a GO-water-GO sandwichlike structure and as a result are stable in water instead of precipitating. However, at high pH, the deprotonated carboxyl groups are very hydrophilic such that individual GO sheets prefer to dissolve in bulk water like a regular salt. The GO aggregates formed at low pH are found to be surface-active and do not exhibit characteristic features of surfactant micelles. Our findings suggest that GO does not behave like conventional surfactants in pH 1 and 14 aqueous solutions. The molecular-level understanding of the solution behavior of GO presented here can facilitate and improve the experimental techniques used to synthesize and sort large, uniform GO dispersions in a solution phase.     

Structural properties of ionic detergent aggregates: a large-scale molecular dynamics study of sodium dodecyl sulfate

The properties of sodium dodecyl sulfate (SDS) aggregates were studied through extensive molecular dynamics simulations with explicit solvent. First, we provide a parametrization of the model within Gromacs. Then, we probe the kinetics of aggregation by starting from a random solution of SDS molecules and letting the system explore its kinetic pathway during the aggregation of multiple units. We observe a structural transition for the surfactant aggregates brought upon by a change in temperature. Specifically, at low temperatures, the surfactants form crystalline aggregates, whereas at elevated temperatures, they form micelles. We also investigate the dependence of aggregation kinetics on surfactant concentration and report on the molecular level structural changes involved in the transition.     

Temperature-induced crystallization in concentrated suspensions of multiarm star polymers: a molecular dynamics study

In this work, we study temperature-induced crystallization in dense suspensions of multiarm star polymers. This is a continuation of a previous study, which identified and studied the emergence of "glassy" amorphous states, in accordance with experimental observations. We performed molecular dynamics simulations on two types of star polymers: 128-arm stars and 64-arm stars dissolved in n-decane in the temperature range of 20-60 degrees C. These supramolecules are modeled as "soft spheres" interacting via a theoretically developed potential of mean field. Both systems attain a crystalline structure with the characteristics of a face-centered-cubic (fcc) crystal beyond a certain temperature. Kinetics is sensitive on initial configuration. Interestingly, kinetic trapping in "temporary" energy wells leads to highly crystalline structures, yet less ordered than their genuine equilibrium fcc structure. This complication illustrates the difficulty in reaching the equilibrium state, which is crystalline at high temperatures. A structural analysis of the final conformations is presented. The effect of size dispersity and star functionality of soft spheres on microstructure is also examined. Both factors influence crystallization and their effect is quantified by our study.     

Electrophoretic properties of highly charged colloids: a hybrid molecular dynamics/lattice Boltzmann simulation study

Using computer simulations, the electrophoretic motion of a positively charged colloid (macroion) in an electrolyte solution is studied in the framework of the primitive model. In this model, the electrolyte is considered as a system of negatively and positively charged microions (counterions and coions, respectively) that are immersed into a structureless medium. Hydrodynamic interactions are fully taken into account by applying a hybrid simulation scheme, where the charged ions (i.e., macroion and electrolyte), propagated via molecular dynamics, are coupled to a lattice Boltzmann (LB) fluid. In a recent electrophoretic experiment by Martin-Molina et al. [J. Phys. Chem. B 106, 6881 (2002)], it was shown that, for multivalent salt ions, the mobility mu initially increases with charge density sigma, reaches a maximum, and then decreases with further increase of sigma. The aim of the present work is to elucidate the behavior of mu at high values of sigma. Even for the case of monovalent microions, a decrease of mu with sigma is found. A dynamic Stern layer is defined that includes all the counterions that move with the macroion while subjected to an external electrical field. The number of counterions in the Stern layer, q(0), is a crucial parameter for the behavior of mu at high values of sigma. In this case, the mobility mu depends primarily on the ratio q(0)/Q (with Q the valency of the macroion). The previous contention that the increase in the distortion of the electric double layer (EDL) with increasing sigma leads to the lowering of mu does not hold for high sigma. In fact, it is shown that the deformation of the EDL decreases with the increase of sigma. The role of hydrodynamic interactions is inferred from direct comparisons to Langevin simulations where the coupling to the LB fluid is switched off. Moreover, systems with divalent counterions are considered. In this case, at high values of sigma the phenomenon of charge inversion is found.     

Characterizing hydrophobicity at the nanoscale: a molecular dynamics simulation study

We use molecular dynamics (MD) simulations of water near nanoscopic surfaces to characterize hydrophobic solute-water interfaces. By using nanoscopic paraffin like plates as model solutes, MD simulations in isothermal-isobaric ensemble have been employed to identify characteristic features of such an interface. Enhanced water correlation, density fluctuations, and position dependent compressibility apart from surface specific hydrogen bond distribution and molecular orientations have been identified as characteristic features of such interfaces. Tetrahedral order parameter that quantifies the degree of tetrahedrality in the water structure and an orientational order parameter, which quantifies the orientational preferences of the second solvation shell water around a central water molecule, have also been calculated as a function of distance from the plate surface. In the vicinity of the surface these two order parameters too show considerable sensitivity to the surface hydrophobicity. The potential of mean force (PMF) between water and the surface as a function of the distance from the surface has also been analyzed in terms of direct interaction and induced contribution, which shows unusual effect of plate hydrophobicity on the solvent induced PMF. In order to investigate hydrophobic nature of these plates, we have also investigated interplate dewetting when two such plates are immersed in water.     

Structure and dynamics of surfactant and hydrocarbon aggregates on graphite: a molecular dynamics simulation study

We have examined the structure and dynamics of sodium dodecyl sulfate (SDS) and dodecane (C12) molecular aggregates at varying surface coverages on the basal plane of graphite via classical molecular dynamics simulations. Our results suggest that graphite-hydrocarbon chain interactions favor specific molecular orientations at the single-molecule level via alignment of the tail along the crystallographic directions. This orientational bias is reduced greatly upon increasing the surface coverage for both molecules due to intermolecular interactions, leading to very weak bias at intermediate surface coverages. Interestingly, for complete monolayers, we find a re-emergent orientational bias. Furthermore, by comparing the SDS behavior with C12, we demonstrate that the charged head group plays a key role in the aggregate structures: SDS molecules display a tendency to form linear file-like aggregates while C12 forms tightly bound planar ones. The observed orientational bias for SDS molecules is in agreement with experimental observations of hemimicelle orientation and provides support for the belief that an initial oriented layer governs the orientation of hemimicellar aggregates.     

Effect of temperature, pressure, and cosolvents on structural and dynamic properties of the hydration shell of SNase: a molecular dynamics computer simulation study

It is now generally agreed that the hydration water and solvational properties play a crucial role in determining the dynamics and hence the functionality of proteins. We present molecular dynamics computer simulation studies on staphylococcal nuclease (SNase) at various temperatures and pressures as well as in different cosolvent solutions containing various concentrations of urea and glycerol. The aim is to provide a molecular level understanding of how different types of cosolvents (chaotropic and kosmotropic) as well as temperature and high hydrostatic pressure modify the structure and dynamics of the hydration water. Taken together, these three intrinsic thermodynamic variables, temperature, pressure, and chemical potential (or activity) of the solvent, are able to influence the stability and function of the protein by protein-solvent dynamic coupling in different ways. A detailed analysis of the structural and dynamical properties of the water and cosolvents at the protein surface (density profile, coordination numbers, hydrogen-bond distribution, average H-bond lifetimes (water-protein and water-water), and average residence time of water in the hydration shell) was carried out, and differences in the structural and dynamical properties of the hydration water in the presence of the different cosolvents and at temperatures between 300 and 400 K and pressures up to 5000 bar are discussed. Furthermore, the results obtained help understand various thermodynamic properties measured for the protein.     

Temperature jump induction of isomerization dynamics of alkali halide clusters

The time resolved dynamics of diffusionless cube → ring isomerization of the Na₄Cl₄ cluster was interrogated by constant energy molecular dynamics simulations, utilizing the first passage time method. The nonreactive isomerization induced by nonselective vibrational excitation is well accounted for in terms of the statistical RRK theory, opening avenues for experimental exploration of time-resolved cluster isomerization dynamics.     

Structural transition to electrolyte-water solvent and changes in the molecular dynamics of water and properties of solutions

A model of concentration transition “ions and complexes in a water structure → ionic and ionicaqueous clusters → polymer structures of salt and crystal hydrate melts” is suggested. The appearance of cluster nanostructures outside the first zone of a waterlike structure is regarded as a general characteristic of solutions. The characteristics of solutions, phase equilibria, and salts of complex composition are interpreted based on this model. Investigation of the complex dielectric constant of electrolytic solutions in the SHF and EHF bands (7–119 GHz) at high concentrations showed that there are two dispersion regions in which the relaxation times differ by a factor of 5–10. Relaxation processes are separated, the numbers of molecules in hydration shells are calculated, and relaxation times are determined for bulky tetrahedral water with hydration shells of ions, for clusters, and for ionicaqueous polymer chains. It is shown that the two structure subsystems of water molecules in concentrated solutions may be described using the limited rotator/generalized diffusion molecular model. Translated fromZhumal Strukturnoi Khimii, Vol. 39, No. 5, pp. 851–863, September–October, 1998.     

Thermal decomposition of a honeycomb-network sheet: A molecular dynamics simulation study

The thermal degradation of a graphene-like two-dimensional honeycomb membrane with bonds undergoing temperature-induced scission is studied by means of Molecular Dynamics simulation using Langevin thermostat. We demonstrate that at lower temperature the probability distribution of breaking bonds is highly peaked at the rim of the membrane sheet whereas at higher temperature bonds break at random everywhere in the hexagonal flake. The mean breakage time τ is found to decrease with the total number of network nodes N by a power law τ ∝ N(-0.5) and reveals an Arrhenian dependence on temperature T. Scission times are themselves exponentially distributed. The fragmentation kinetics of the average number of clusters can be described by first-order chemical reactions between network nodes n(i) of different coordination. The distribution of fragments sizes evolves with time elapsed from initially a δ-function through a bimodal one into a single-peaked again at late times. Our simulation results are complemented by a set of 1st-order kinetic differential equations for n(i) which can be solved exactly and compared to data derived from the computer experiment, providing deeper insight into the thermolysis mechanism.