A first-principles study of hydrogen surface coverage on δ-Pu (100), (111), and (110) surfaces.

Hydriding corrosion of plutonium leads to surface cracking, pitting, and ultimately structural failure. Laboratory experiments demonstrate that hydriding begins on the surface or near the subsurface of plutonium. However, there has not yet been a systematic evaluation of hydrogen surface coverage on plutonium. In this work, we compute the surface energies of the low facet surfaces of face-centered cubic δ-Pu. The adsorption free energies of expected hydrogen structures at low and high coverage are presented along with the likely progression for filling sites as the H2 partial pressure increases. Implications for near-equilibrium pressure hydride nucleation and non-equilibrium millibar pressure hydriding are discussed.

Surface force measurements and simulations of mussel-derived peptide adhesives on wet organic surfaces.

Translating sticky biological molecules-such as mussel foot proteins (MFPs)-into synthetic, cost-effective underwater adhesives with adjustable nano- and macroscale characteristics requires an intimate understanding of the glue's molecular interactions. To help facilitate the next generation of aqueous adhesives, we performed a combination of surface forces apparatus (SFA) measurements and replica-exchange molecular dynamics (REMD) simulations on a synthetic, easy to prepare, Dopa-containing peptide (MFP-3s peptide), which adheres to organic surfaces just as effectively as its wild-type protein analog. Experiments and simulations both show significant differences in peptide adsorption on CH3-terminated (hydrophobic) and OH-terminated (hydrophilic) self-assembled monolayers (SAMs), where adsorption is strongest on hydrophobic SAMs because of orientationally specific interactions with Dopa. Additional umbrella-sampling simulations yield free-energy profiles that quantitatively agree with SFA measurements and are used to extract the adhesive properties of individual amino acids within the context of MFP-3s peptide adhesion, revealing a delicate balance between van der Waals, hydrophobic, and electrostatic forces.

Cassandra: An open source Monte Carlo package for molecular simulation.

Cassandra is an open source atomistic Monte Carlo software package that is effective in simulating the thermodynamic properties of fluids and solids. The different features and algorithms used in Cassandra are described, along with implementation details and theoretical underpinnings to various methods used. Benchmark and example calculations are shown, and information on how users can obtain the package and contribute to it are provided. © 2017 Wiley Periodicals, Inc.

Discrete Fractional Component Monte Carlo Simulation Study of Dilute Nonionic Surfactants at the Air-Water Interface.

We present a newly developed Monte Carlo scheme to predict bulk surfactant concentrations and surface tensions at the air-water interface for various surfactant interfacial coverages. Since the concentration regimes of these systems of interest are typically very dilute (≪10-5 mol. frac.), Monte Carlo simulations with the use of insertion/deletion moves can provide the ability to overcome finite system size limitations that often prohibit the use of modern molecular simulation techniques. In performing these simulations, we use the discrete fractional component Monte Carlo (DFCMC) method in the Gibbs ensemble framework, which allows us to separate the bulk and air-water interface into two separate boxes and efficiently swap tetraethylene glycol surfactants C10E4 between boxes. Combining this move with preferential translations, volume biased insertions, and Wang-Landau biasing vastly enhances sampling and helps overcome the classical "insertion problem", often encountered in non-lattice Monte Carlo simulations. We demonstrate that this methodology is both consistent with the original molecular thermodynamic theory (MTT) of Blankschtein and co-workers, as well as their recently modified theory (MD/MTT), which incorporates the results of surfactant infinite dilution transfer free energies and surface tension calculations obtained from molecular dynamics simulations.

Communication: an existence test for dividing surfaces without recrossing.

The claim that Grote-Hynes theory (GHT), when it provides accurate rates, is equivalent to multidimensional variational transition state theory (VTST) has been debated for decades with convincing arguments on both sides. For the two theories to be equivalent a perfect dividing surface with no recrossing must exist. We describe an easily implemented test employing deterministic microcanonical (NVE) trajectories which can identify situations where no perfect dividing surface exists and thereby potentially falsify the claim of equivalence. We use this test to reach data-supported conclusions about the relationship between GHT and VTST.

Reaction Ensemble Monte Carlo Simulations of CO2 Absorption in the Reactive Ionic Liquid Triethyl(octyl)phosphonium 2-Cyanopyrrolide.

The absorption of CO2 into an aprotic heterocyclic anion ionic liquid (IL) is modeled using reaction ensemble Monte Carlo (RxMC) with the semigrand reaction move. RxMC has previously been unable to sample chemical equilibrium involving molecular ions in nanostructured liquids due to the high free-energy requirements to open and close cavities and restructure the surrounding environment. Our results are validated by experiments in the modeled IL, triethyl(octyl)phosphonium 2-cyanopyrrolide ([P2228][cnp]), and in a close analog with longer alkyl chains on the cation. Heats of absorption and reaction from both experiment and simulation are exothermic and of comparable magnitude. Replacing experimental Henry's constants with their simulated counterparts improves the accuracy of a Langmuir-type model at moderate pressures. Nonidealities that affect chemical equilibrium are identified and calculated with high precision.

Reaction Ensemble Monte Carlo Simulation of Xylene Isomerization in Bulk Phases and under Confinement.

The original reaction move for the reaction ensemble Monte Carlo (RxMC) method is adapted to align both the position and orientation of inserted product molecules and deleted reactant molecules. The accuracy and efficiency of this move is demonstrated for xylene isomerization in vapor, liquid, and supercritical phases. Classical RxMC requires the ideal gas free energy of reaction ΔGrxnideal as an input. We compare three methods for computing ΔGrxnideal: using tabulated enthalpies and entropies of formation, using the harmonic oscillator and rigid rotor approximations and using QM/MM alchemical transformation combined with multistate Bennett acceptance ratio. We find that the tabulated free energies of reaction give the best agreement with experimental equilibrium compositions in bulk fluids. RxMC simulations in a carbon nanotube with an inner diameter of approximately 6 Å show that p-xylene becomes the dominant isomer under confinement, an effect consistent with the production of p-xylene in the zeolite ZSM-5. We also show that o-xylene becomes the dominant isomer in nanotubes with an inner diameter of 7-8 Å. We find that both m- and p-xylene exhibit a loss of rotational entropy in nanotubes of this diameter, effectively allowing o-xylene to fit into cavities inaccessible to the other isomers.

Easy transition path sampling methods: flexible-length aimless shooting and permutation shooting.

We present new algorithms for conducting transition path sampling (TPS). Permutation shooting rigorously preserves the total energy and momentum of the initial trajectory and is simple to implement even for rigid water molecules. Versions of aimless shooting and permutation shooting that use flexible-length trajectories have simple acceptance criteria and are more computationally efficient than fixed-length versions. Flexible-length permutation shooting and inertial likelihood maximization are used to identify the reaction coordinate for vacancy migration in a two-dimensional trigonal crystal of Lennard-Jones particles. The optimized reaction coordinate eliminates nearly all recrossing of the transition state dividing surface.

Transmission Coefficients, Committors, and Solvent Coordinates in Ion-Pair Dissociation.

From a hypothetical perfect dividing surface, all trajectories commit to opposite basins in forward and backward time without recrossing, transition state theory is exact, the transmission coefficient is one, and the committor distribution is perfectly focused at 1/2. However, chemical reactions in solution and other real systems often have dynamical trajectories that recross the dividing surface. To separate true dynamical effects from effects of a nonoptimal dividing surface, the dividing surface and/or reaction coordinate should be optimized before computing transmission coefficients. For NaCl dissociation in TIP3P water, we show that recrossing persists even when the 1/2-committor surface itself is used as the dividing surface, providing evidence that recrossing cannot be fully eliminated from the dynamics for any configurational coordinate. Consistent with this finding, inertial likelihood maximization finds a combination of ion-pair distance and two solvent coordinates that improves the committor distribution and increases the transmission coefficient relative to those for ion-pair distance alone, but recrossing is not entirely eliminated. Free energy surfaces for the coordinates identified by inertial likelihood maximization show that the intrinsic recrossing stems from anharmonicity and shallow intermediates that remain after dimensionality reduction to the dynamically important variables.