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Our new simulation scheme in isosurface−isothermal−isobaric ensemble [Eslami, H.; Mozaffari, F.; Moghadasi, J.; Müller-Plathe, F. J. Chem. Phys.2008, 129, 194702], developed to simulate confined fluids in equilibrium with bulk, is applied to simulate polyamide-6,6 oligomers confined between graphite surfaces. The reverse nonequilibrium molecular dynamics simulation technique is employed to shear the graphite surfaces. In this work, six confined systems, with different surface separations, as well as the bulk fluid are simulated. Our results show a viscosity increase with respect to the bulk fluid, with decreasing distance between surfaces. Also, the calculated viscosities of the confined systems show an oscillatory behavior with maxima corresponding to well-formed layers between the surfaces. We observe a substantial slip at the surfaces, with the slip length depending on the shear rate and on the slit width. The slip length and the slip velocity show oscillatory behavior with out-of-phase oscillations with respect to the solvation force oscillations. Moreover, the temperature difference between coldest and hottest parts of the simulation box depends on the shear rate and on the layering effect (solvation force oscillations). An analysis of oligomer deformation under flow shows preferential alignment of oligomers parallel to the surfaces with increasing shear rate. [ABSTRACT FROM AUTHOR]

A molecular dynamics simulation method with coupling to an external bath is used to simulate polyamide-6,6 trimers confined between graphite surfaces. In this simulation method, the temperature and the parallel component of pressure are kept fixed, and the distance between the confining graphite surfaces is changed to achieve equilibrium. The simulation results on the oscillatory behavior of solvation force, the number density of confined oligomers, and stepwise variation of the oligomer numbers as a function of distance between the confining graphite surfaces are reported and discussed. The hydrogen bonding in confined oligomers has also been studied in detail, and it is shown that hydrogen-bond formation depends on the layering effect and on the geometrical restrictions and reveals an oscillatory behavior like the solvation force oscillations. The autocorrelation functions for NH, CO, and end-to-end vectors are also studied, and it is concluded that the confined fluid has a considerably lower relaxation time than that of the bulk fluid, and the relaxation times for confined fluid show an oscillatory behavior with maxima corresponding to well-formed structures parallel to the surfaces. The study of local dynamics via calculating the autocorrelation functions for bins parallel to the surfaces reveals that the fluid layers close to the surfaces have higher relaxation times than the fluid in the central region. Our calculated center-of-mass diffusion coefficients also show oscillatory behavior with out-of-phase oscillations with respect to the solvation force oscillations. [ABSTRACT FROM AUTHOR]

We studied the thermal diffusion behavior of mixtures of benzene and heptane isomers by reverse nonequilibrium molecular dynamics. For n-heptane/benzene mixtures, we investigated the concentration dependence of the Soret coefficient. The Soret coefficient for equimolar mixtures of the three heptane isomers 3-methylhexane, 2,3-dimethylpentane, and 2,4-dimethylpentane in benzene has been calculated. Compared to the experimental data, the simulation results show the same trend in dependence of the mole fraction and degree of branching. The negative Soret coefficient indicates the enrichment of alkanes in the warm side. In the case of the heptane isomers in benzene, we could study the influence of the difference in shape and size on the thermal diffusion behavior at constant mass. In the simulation as well as in the experiment, we found that the Soret coefficients become higher with increasing degree of branching. Such behavior cannot be explained only by mass and size effects. The effect of the molecular shape needs to be considered additionally. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations are used to study the microscopic structure and dynamics of cations bound to cucurbit6uril (CB6) in water and in aqueous solutions of sodium, potassium, and calcium chloride. The molarities are 0.183 M for the salts and 0.0184 M for CB6. The cations bind only to CB6 carbonyl oxygens. They are never found inside the CB6 cavity. Complexes with Naand Kmostly involve one cation, whereas with Ca2single- and double-cation complexes are formed in similar proportions. The binding dynamics strongly depends on the type of cation. A smaller size or higher charge increases the residence time of a cation at a given carbonyl oxygen. When bound to CB6, sodium and potassium cations jump mainly between nearest or second-nearest neighbors. Calcium shows no hopping dynamics. It is coordinated predominantly by one CB6 oxygen. A few water molecules (zero to four) can occupy the CB6 cavity, which is limited by the CB6 oxygen faces. Their residence time is hardly influenced by sodium and potassium ions. In the case of calcium the residence time of the inner water increases notably. A simple structural model for the cation activity as “lids” over the CB6 portal cannot, however, be identified. The slowing of the water exchange by the ions is a consequence of the generally slower dynamics in their presence and of their stable solvation shells. [ABSTRACT FROM AUTHOR]