David J. Keffer

Comparison of the Hydration and Diffusion of Protons in Perfluorosulfonic Acid Membranes with Molecular Dynamics Simulations

Classical molecular dynamics (MD) simulations were performed to determine the hydrated morphology and hydronium ion diffusion coefficients in two different perfluorosulfonic acid (PFSA) membranes as functions of water content. The structural and transport properties of 1143 equivalent weight (EW) Nafion, with its relatively long perfluoroether side chains, are compared to the short-side-chain (SSC) PFSA ionomer at an EW of 977. The separation of the side chains was kept uniform in both ionomers consisting of -(CF 2) 15- units in the backbone, and the degree of hydration was varied from 5 to 20 weight % water. The MD simulations indicated that the distribution of water clusters is more dispersed in the SSC ionomer, which leads to a more connected water-channel network at the low water contents. This suggests that the SSC ionomer may be more inclined to form sample-spanning aqueous domains through which transport of water and protons may occur. The diffusion coefficients for both hydronium ions and water molecules were calculated at hydration levels of 4.4, 6.4, 9.6, and 12.8 H 2O/SO 3H for each ionomer. When compared to experimental proton diffusion coefficients, this suggests that as the water content is increased the contribution of proton hopping to the overall proton diffusion increases.

Unidirectional and single-file diffusion in AlPO4-5: molecular dynamics investigations

Canonical ensemble molecular dynamics simulations of Lennard-Jones methane and ethane are conducted in an atomistic model of AlPO4-5, a molecular sieve with approximately cylindrical channels of diameter 7·3 A. Methane molecules are able to pass each other in the nanopore and exhibit unidirectional but otherwise ordinary diffusion along the channel axis, with the mean-square displacement directly proportional to time, and a diffusion coefficient calculated at a loading of 0·7 molecules per unit cell at 295 K of 4·70 × 10-4 cm2 s-1. Ethane molecules cannot pass each other easily in the nanopore and for short times exhibit single-file diffusion, i.e., the mean-square displacement is proportional to the square root of the time. After longer times, contributions of ordinary unidirectional diffusion are observed due to the nonzero probability of passing. A slightly larger molecule exhibits pure single-file diffusion. The single-file mobility for the large molecule at 0·7 molecule per unit cell and 295 K is 1·5...

Rheological and structural studies of liquid decane, hexadecane, and tetracosane under planar elongational flow using nonequilibrium molecular-dynamics simulations

We report for the first time rheological and structural properties of liquid decane, hexadecane, and tetracosane using nonequilibrium molecular-dynamics (NEMD) simulations under planar elongational flow (PEF). The underlying NEMD algorithm employed is the so-called p-SLLOD algorithm [C. Baig, B. J. Edwards, D. J. Keffer, and H. D. Cochran, J. Chem. Phys. 122, 114103 (2005)]. Two elongational viscosities are measured, and they are shown not to be equal to each other, indicating two independent viscometric functions in PEF. With an appropriate definition, it is observed that the two elongational viscosities converge to each other at very low elongation rates, i.e., in the Newtonian regime. For all three alkanes, tension-thinning behavior is observed. At high elongation rates, chains appear to be fully stretched. This is supported by the result of the mean-square end-to-end distance of chains (R(ete2)) and the mean-square radius of gyration of chains (R(g2)), and further supported by the result of the intramolecular Lennard-Jones (LJ) potential energy. It is also observed that (R(ete2)) and (R(g2)) show a different trend as a function of strain rate from those in shear flow: after reaching a plateau value, (R(ete2)) and (R(g2)) are found to increase further as elongation rate increases. A minimum in the hydrostatic pressure is observed for hexadecane and tetracosane at about epsilon(msigma2/epsilon)1/2=0.02. This phenomenon is shown to be associated with the intermolecular LJ potential energy. The bond-bending and torsional energies display similar trends, but a different behavior is observed for the bond-stretching energy. An important observation common in these three bonded-intramolecular interactions is that all three modes are suppressed to a small value at high elongation rates. We conjecture that a liquid-crystal-like, nematic structure is present in these systems at high elongation rates, which is characterized by a strong chain alignment with a fully stretched conformation.

A proper approach for nonequilibrium molecular dynamics simulations of planar elongational flow

We present nonequilibrium molecular dynamics simulations of planar elongational flow (PEF) by an algorithm proposed by Tuckerman et al. [J. Chem. Phys. 106, 5615 (1997)] and theoretically elaborated by Edwards and Dressler [J. Non-Newtonian, Fluid Mech. 96, 163 (2001)], which we shall call the proper-SLLOD algorithm, or p-SLLOD for short. [For background on names of algorithms see W. G. Hoover, D. J. Evans, R. B. Hickman, A. J. C. Ladd, W. T. Ashurst, and B. Moran, Phys. Rev. A 22, 1690 (1980) and D. J. Evans and G. P. Morriss, Phys. Rev. A 30, 1528 (1984).] We show that there are two sources for the exponential growth in PEF of the total linear momentum of the system in the contracting direction, which has been previously observed using the so-called SLLOD algorithm. The first comes from the SLLOD algorithm itself, and the second from the implementation of the Kraynik and Reinelt [Int. J. Multiphase Flow 18, 1045 (1992)] boundary conditions. Using the p-SLLOD algorithm (to eliminate the first source) implemented with our simulation strategy (to eliminate the second) in PEF simulations, we no longer observe the exponential growth. By analyzing the equations of motion, we also demonstrate that both the SLLOD and the DOLLS algorithms are intrinsically unsuitable for representing a nonequilibrium system with elongational flow. However, the p-SLLOD algorithm has a rigorously canonical structure in laboratory phase space, and thus can represent a nonequilibrium system not only for elongational flow but also for a general flow.

The Effect of Nanopore Shape on the Structure and Isotherms of Adsorbed Fluids

A Grand Canonical Monte Carlo simulation method is used to determine the adsorption isotherms, interaction energies, entropies, and density distribution of a Lennard-Jones fluid adsorbed in smooth-walled nanopores of varying size and shape. We specifically include very crowded pores, where packing effects are important. Differences in the isotherms of slit, cylindrical, and spherical nanopores of varying sizes can be explained in terms of the adsorbate-adsorbate interaction energy, the adsorbate-pore interaction energy, and the density profiles, which influence the balance between the former and the latter energy contributions. The expectation from low loading studies that the most energetically favorable adsorbate-pore interactions maximize adsorption is not borne out at intermediate and higher loadings. Instead, the relationships between adsorbed amounts and pore size and shape are found to be strong functions of the depth and steepness of the external potential, the extent to which adsorbate-adsorbate repulsion establishes short range fluid order, and the accessible pore volume. This study has implications for high pore density processes in nanoporous materials, such as zeolite catalysis, separations, and templating in zeolite synthesis.

Rheological and structural studies of linear polyethylene melts under planar elongational flow using nonequilibrium molecular dynamics simulations

We present various rheological and structural properties of three polyethylene liquids, C50H102, C78H158, and C128H258, using nonequilibrium molecular dynamics simulations of planar elongational flow. All three melts display tension-thinning behavior of both elongational viscosities, eta1 and eta2. This tension thinning appears to follow the power law with respect to the elongation rate, i.e., eta approximately epsilon(b), where the exponent b is shown to be approximately -0.4 for eta1 and eta2. More specifically, b of eta1 is shown to be slightly larger than that of eta2 and to increase in magnitude with the chain length, while b of eta2 appeared to be independent of the chain length. We also investigated separately the contribution of each mode to the two elongational viscosities. For all three liquids, the intermolecular Lennard-Jones (LJ), intramolecular LJ, and bond-stretching modes make positive contributions to both eta1 and eta2, while the bond-torsional and bond-bending modes make negative contributions to both eta1 and eta2. The contribution of each of the five modes decreases in magnitude with increasing elongation rate. The hydrostatic pressure shows a clear minimum at a certain elongation rate for each liquid, and the elongation rate at which the minimum occurs appears to increase with the chain length. The behavior of the hydrostatic pressure with respect to the elongation rate is shown to correlate with the intermolecular LJ energy from a microscopic viewpoint. On the other hand, R(ete)2 and R(g)2 appear to be correlated with the intramolecular LJ energy. The study of the effect of the elongational field on the conformation tensor c shows that the degree of increase of tr(c)-3 with the elongation rate becomes stronger as the chain length increases. Also, the well-known linear reaction between sigma and c does not seem to be satisfactory. It seems that a simple relation between sigma and c would not be valid, in general, for arbitrary flows.

A validation of the p-SLLOD equations of motion for homogeneous steady-state flows

A validation of the p-SLLOD equations of motion for nonequilibrium molecular dynamics simulation under homogeneous steady-state flow is presented. We demonstrate that these equations generate the correct center-of-mass trajectory of the system, are completely compatible with (and derivable from) Hamiltonian dynamics, satisfy an appropriate energy balance, and require no fictitious external force to generate the required homogeneous flow. It is also shown that no rigorous derivation of the SLLOD equations exists to date.

An Examination of the Validity of Nonequilibrium Molecular-dynamics Simulation Algorithms for Arbitrary Steady-state Flows

Nonlinear-response theory of nonequilibrium molecular-dynamics simulation algorithms is considered under the imposition of an arbitrary steady-state flow field. It is demonstrated that the SLLOD and DOLLS algorithms cannot be used for general flows, although the SLLOD algorithm is rigorous for planar Couette flow. Following the same procedure used to establish SLLOD as the valid algorithm for planar Couette flow [D. J. Evans and E. P. Morriss, Phys. Rev. A 30, 1528 (1984)], it is demonstrated that the p-SLLOD algorithm is valid for arbitrary flows and produces the correct nonlinear response of the viscous pressure tensor.

Effect of charge distribution on RDX adsorption in IRMOF-10.

Quantum mechanical (QM) calculations, classical grand canonical Monte Carlo (GCMC) simulations, and classical molecular dynamics (MD) simulations are performed to test the effect of charge distribution on hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) adsorption and diffusion in IRMOF-10. Several different methods for mapping QM electron distributions onto atomic point charges are explored, including the electrostatic potential (ESP) method, Mulliken population analysis, Lowdin population analysis, and natural bond orbital analysis. Classical GCMC and MD simulations of RDX in IRMOF-10 are performed using 15 combinations of charge sources of RDX and IRMOF-10. As the charge distributions vary, interaction potential energies, the adsorption loading, and the self-diffusivities are significantly different. None of the 15 combinations are able to quantitatively capture the dependence of the energy of adsorption on local configuration of RDX as observed in the QM calculations. We observe changes in the charge distributions of RDX and IRMOF-10 with the introduction of an RDX molecule into the cage. We also observe a large dispersion contribution to the interaction energy from QM calculations that is not reproduced in the classical simulations, indicating that the source of discrepancy may not lie exclusively with the assignment of charges.

Computational Chemistry for Molecular Electronics

We present a synergetic effort of a group of theorists to characterize a molecular electronics device through a multiscale modeling approach. We combine electronic-structure calculations with molecular dynamics and Monte Carlo simulations to predict the structure of self-assembled molecular monolayers on a metal surface. We also develop a novel insight into molecular conductance, with a particular resolution of its fundamental channels, which stresses the importance of a complete molecular structure description of all components of the system, including the leads, the molecule, and their contacts. Both molecular dynamics and electron transport simulations imply that knowledge of detailed molecular structure and system geometry are critical for successful comparison with carefully performed experiments. We illustrate our findings with benzenedithiolate molecules in contact with gold.