Publications

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Anion hydration is complicated by H-bond between neighboring water molecules in addition to H-bond donation to the anion. This situation leads to competing structures and anharmonic vibrations for simple clusters like (H2O)nCl-. This study applies quasi-chemical theory to study anion hydration and exploits dynamics calculations on isolated clusters to account for anharmonicity. Comparing singly hydrated halide clusters, classic H-bond donation to the anion occurs for F-, while Cl- clusters exhibit flexible dipole-dominated interactions. The predicted Cl- – F- hydration free energy difference agrees with experiment, a significant theoretical step for addressing issues like Hofmeister ranking and selectivity in ion channels.

EmrE is a small, homodimeric membrane transporter that exploits the established pH gradient across the E. coli inner membrane to export polyaromatic cations that might otherwise inhibit cellular growth. While herculean efforts through experimental studies have established many fundamental facts about the specificity and rate of substrate transport in EmrE, the low resolution of the available structures have hampered efforts to tie those findings to the EmrE coupling mechanism between proton and small molecule substrates. Here we present a full three-dimensional structure of EmrE optimized against available cyro-EM data to delineate the critical interactions by which EmrE regulates its conformation. We use the generated structural model to conduct equilibrium and nonequilibrium molecular dynamics simulations to probe EmrE dynamics under different substrate loading states, representing different states in the transport cycle. The model is stable under extended simulation, and reveals that water dynamics within the EmrE lumen change substantially with the loading state. The water dynamics cause hydrogen bonding networks to shift radically when the protonation states change for a pair of solvent-exposed glutamate residues (E14) within the lumen of the transporter, which are proposed to act as proton binding sites during the transport cycle. One specific hydrogen bond from a tyrosine (Y60) of one monomer to a glutamate (E14) on the opposite monomer is especially critical, as it locks the protein conformation when the glutamate is deprotonated. Furthermore, the hydrogen bond provided by Y60 lowers the pK_a of the interacting glutamate relative to its partner on the opposite monomer such that it will protonate second, establishing the need for both glutamates to be protonated for the hydrogen bond to break and a substrate-free transition to take place.

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Li+ transport within a solid electrolyte interphase (SEI) in lithium ion batteries has challenged molecular dynamics (MD) studies due to limited compositional control of that layer. In recent years, experiments and ab initio simulations have identified dilithium ethylene dicarbonate (Li2EDC) as the dominant component of SEI layers. Here, we adopt a parameterized, non-polarizable MD force field for Li2EDC to study transport characteristics of Li+ in this model SEI layer at moderate temperatures over long times. The observed correlations are consistent with recent MD results using a polarizable force field, suggesting that this non-polarizable model is effective for our purposes of investigating Li+ dynamics. Mean-squared displacements distinguish three distinct Li+ transport regimes in EDC-ballistic, trapping, and diffusive. Compared to liquid ethylene carbonate (EC), the nanosecond trapping times in EDC are significantly longer and naturally decrease at higher temperatures. New materials developed for fast-charging Li-ion batteries should have a smaller trapping region. The analyses implemented in this paper can be used for testing transport of Li+ ion in novel battery materials. Non-Gaussian features of van Hove self-correlation functions for Li+ in EDC, along with the mean-squared displacements, are consistent in describing EDC as a glassy material compared with liquid EC. Vibrational modes of Li+ ion, identified by MD, characterize the trapping and are further validated by electronic structure calculations. Some of this work appeared in an extended abstract and has been reproduced with permission from ECS Transactions, 77, 1155-1162 (2017). Copyright 2017, Electrochemical Society, INC.

The limited flux and selectivities of current carbon dioxide membranes and the high costs associated with conventional absorption-based CO2 sequestration call for alternative CO2 separation approaches. Here we describe an enzymatically active, ultra-thin, biomimetic membrane enabling CO2 capture and separation under ambient pressure and temperature conditions. The membrane comprises a ~18-nm-thick close-packed array of 8 nm diameter hydrophilic pores that stabilize water by capillary condensation and precisely accommodate the metalloenzyme carbonic anhydrase (CA). CA catalyzes the rapid interconversion of CO2 and water into carbonic acid. By minimizing diffusional constraints, stabilizing and concentrating CA within the nanopore array to a concentration 10× greater than achievable in solution, our enzymatic liquid membrane separates CO2 at room temperature and atmospheric pressure at a rate of 2600 GPU with CO2/N2 and CO2/H2 selectivities as high as 788 and 1500, respectively, the highest combined flux and selectivity yet reported for ambient condition operation.

Anthrax toxin consists of a cation channel and two protein factors. Translocation of the anthrax protein factors from endosomal to the cytosolic compartment is a complex process which utilizes the cation channel. An atomically detailed understanding of the function of the anthrax translocation machinery is incomplete. We report atomically detailed simulations of the lethal factor and channel mutants. Kinetic and thermodynamic properties of early events in the translocation process are computed within the Milestoning theory and algorithm. Several mutants of the channel illustrate that long-range electrostatic interactions provide the dominant driving force for translocation. No external energy input is required because the lower pH in the endosome relative to the cytosol drives the initial translocation process forward. Channel mutants with variable sizes cause smaller effects on translocation events relative to charge manipulations. Comparison with available experimental data is provided.

EmrE is a small, homodimeric membrane transporter that exploits the established electrochemical proton gradient across the Escherichia coli inner membrane to export toxic polyaromatic cations, prototypical of the wider small-multidrug resistance transporter family. While prior studies have established many fundamental aspects of the specificity and rate of substrate transport in EmrE, low resolution of available structures has hampered identification of the transport coupling mechanism. Here we present a complete, refined atomic structure of EmrE optimized against available cryo-electron microscopy (cryo-EM) data to delineate the critical interactions by which EmrE regulates its conformation during the transport process. With the model, we conduct molecular dynamics simulations of the transporter in explicit membranes to probe EmrE dynamics under different substrate loading and conformational states, representing different intermediates in the transport cycle. The refined model is stable under extended simulation. The water dynamics in simulation indicate that the hydrogen-bonding networks around a pair of solvent-exposed glutamate residues (E14) depend on the loading state of EmrE. One specific hydrogen bond from a tyrosine (Y60) on one monomer to a glutamate (E14) on the opposite monomer is especially critical, as it locks the protein conformation when the glutamate is deprotonated. The hydrogen bond provided by Y60 lowers the pKa of one glutamate relative to the other, suggesting both glutamates should be protonated for the hydrogen bond to break and a substrate-free transition to take place. These findings establish the molecular mechanism for the coupling between proton transfer reactions and protein conformation in this proton-coupled secondary transporter.

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Electrochemical double-layer capacitances of charged carbon nanotube (CNT) forests with tetraethyl ammonium tetrafluoro borate electrolyte in propylene carbonate are studied on the basis of molecular dynamics simulation. Direct molecular simulation of the filling of pore spaces of the forest is feasible even with realistic, small CNT spacings. The numerical solution of the Poisson equation based on the extracted average charge densities then yields a regular experimental dependence on the width of the pore spaces, in contrast to the anomalous pattern observed in experiments on other carbon materials and also in simulations on planar slot-like pores. The capacitances obtained have realistic magnitudes but are insensitive to electric potential differences between the electrodes in this model. This agrees with previous calculations on CNT forest supercapacitors, but not with experiments which have suggested electrochemical doping for these systems. Those phenomena remain for further theory/modeling work.

The role that van der Waals (vdW) attractive forces play in the hydration and association of atomic hydrophobic solutes such as argon (Ar) in water is reanalyzed using the local molecular field (LMF) theory of those interactions. In this problem, solute vdW attractive forces can reduce or mask hydrophobic interactions as measured by contact peak heights of the ArAr correlation function compared to reference results for purely repulsive core solutes. Nevertheless, both systems exhibit a characteristic hydrophobic inverse temperature behavior in which hydrophobic association becomes stronger with increasing temperature through a moderate temperature range. The new theoretical approximation obtained here is remarkably simple and faithful to the statistical mechanical LMF assessment of the necessary force balance. Our results extend and significantly revise approximations made in a recent application of the LMF approach to this problem and, unexpectedly, support a theory of nearly 40 years ago.

Laying a basis for molecularly specific theory for the mobilities of ions in solutions of practical interest, we report a broad survey of velocity autocorrelation functions (VACFs) of Li+ and PF6- ions in water, ethylene carbonate, propylene carbonate, and acetonitrile solutions. We extract the memory function, γ(t), which characterizes the random forces governing the mobilities of ions. We provide comparisons controlling for the effects of electrolyte concentration and ion-pairing, van der Waals attractive interactions, and solvent molecular characteristics. For the heavier ion (PF6-), velocity relaxations are all similar: negative tail relaxations for the VACF and a clear second relaxation for γt, observed previously also for other molecular ions and with n-pentanol as the solvent. For the light Li+ ion, short time-scale oscillatory behavior masks simple, longer time-scale relaxation of γt. But the corresponding analysis of the solventberg Li+H2O4 does conform to the standard picture set by all the PF6- results.

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Progress in understanding liquid ethylene carbonate (EC) and propylene carbonate (PC) on the basis of molecular simulation, emphasizing simple models of interatomic forces, is reviewed. Results on the bulk liquids are examined from the perspective of anticipated applications to materials for electrical energy storage devices. Preliminary results on electrochemical double-layer capacitors based on carbon nanotube forests and on model solid-electrolyte interphase (SEI) layers of lithium ion batteries are considered as examples. The basic results discussed suggest that an empirically parameterized, non-polarizable force field can reproduce experimental structural, thermodynamic, and dielectric properties of EC and PC liquids with acceptable accuracy. More sophisticated force fields might include molecular polarizability and Buckingham-model description of inter-atomic overlap repulsions as extensions to Lennard-Jones models of van der Waals interactions. Simple approaches should be similarly successful also for applications to organic molecular ions in EC/PC solutions, but the important case of Li+ deserves special attention because of the particularly strong interactions of that small ion with neighboring solvent molecules. To treat the Li+ ions in liquid EC/PC solutions, we identify interaction models defined by empirically scaled partial charges for ion-solvent interactions. The empirical adjustments use more basic inputs, electronic structure calculations and ab initio molecular dynamics simulations, and also experimental results on Li+ thermodynamics and transport in EC/PC solutions. Application of such models to the mechanism of Li+ transport in glassy SEI models emphasizes the advantage of long time-scale molecular dynamics studies of these non-equilibrium materials.