Identifying Local Interfaces.

While interfacial regions often occupy a relatively small portion of a system, physical and chemical processes often proceed differently within them. It is therefore useful to identify interfacial regions to answer many questions in physical chemistry. Thermodynamic phases are often described by their density and local structure; therefore, interfacial regions can then be defined as regions with densities and structures that deviate from the properties of the neighboring phases. Using this perspective of local density and structure around an atom, we describe a "directed search cone" method that has proved useful in identifying atoms that sit at the interface between two regions of a system. We call the set of atoms found to be sitting on the surface "leading atoms", and we construct an interface from these atoms that we call the "leading layer interface". We demonstrate the leading layer interface on solid-vacuum, liquid-vacuum, and liquid-vapor systems. In addition to presenting our method and example calculations, we discuss some observations of local density fluctuations that may be useful for the analysis of heterogeneous systems. Depending on the circumstances, there are various perspectives of an interface that may be insightful, and our leading layer interface will be useful in situations where the correlation between interfacial dynamics and local molecular composition is investigated.

pH-Dependent Compaction of the Intrinsically Disordered Poly-E Motif in Titin.

The conformational sensitivity of intrinsically disordered proteins to shifts in pH due to their high degree of charged residues has been recognized for well over a decade. However, the role of the non-ionizable residues in this pH sensitivity remains poorly understood. Our lab has been investigating the pH sensitivity of the poly-E motifs of the PEVK region of the muscle protein titin, which provides an ideal model system to explore this question. Using a series of 15-amino acid peptides derived from one of the poly-E motif sequences, we have investigated the role of side-chain chemistry in the conformational flexibility of this region. Our results demonstrate that aromatic side chains and proline content are the two variables that most influence pH sensitivity. The introduction of aromatic side chains resulted in a more collapsed structure, even at pH 7, while the removal of prolines resulted in a higher degree of pH sensitivity. These results highlight the importance of considering the impact of non-ionizable residues on IDP function, especially when considering the impact of pH on conformational flexibility.

Non-isoplethic measurement on the solid-liquid-vapor equilibrium of binary mixtures at cryogenic temperatures.

We measured the solid-liquid-vapor (SLV) equilibrium of binary mixtures during experiments that alternated between cooling the mixture and injecting the more-volatile component into the sample chamber; thus, the composition of the mixture changed (non-isoplethic) throughout the experiment. Four binary mixtures were used in the experiments to represent mixtures with miscible solid phases (N2/CO) and barely miscible solid solutions (N2/C2H6), as well as mixtures with intermediate solid miscibility (N2/CH4 and CO/CH4). We measured new SLV pressure data for the binary mixtures, except for N2/CH4, which are also available in the literature for verification in this work. While these mixtures are of great interest in planetary science and cryogenics, the resulting pressure data are also needed for modeling purposes. We found the results for N2/CH4 to be consistent with the literature. The resulting new SLV curve for CO/CH4 shows similarities to N2/CH4. Both have two density inversion points (bracketing the temperature range where the solid floats). This result is important for places such as Pluto, Triton, and Titan, where these mixtures exist in vapor, liquid, and solid phases. Based on our experiments, the presence of a eutectic is unlikely for the N2/CH4 and CO/CH4 systems. An azeotrope with or without a peritectic is likely, but further investigations are needed to confirm. The N2/CO system does not have a density inversion point, as the ice always sinks in its liquid. For N2/C2H6, new SLV pressure data were measured near each triple point of the pure components.

Long-ranged heterogeneous structure in aqueous solutions of the deep eutectic solvent choline and geranate at the liquid-vapor interface.

The deep eutectic solvent choline and geranate (CAGE) has shown promise in many therapeutic applications. CAGE facilitates drug delivery through unique modes of action making it an exciting therapeutic option. We examine the behavior of aqueous CAGE solutions at a liquid-vapor interface. We find that the liquid-vapor interface induces large oscillations in the density, which corresponds to spontaneous segregation into regions enriched with geranate and geranic acid and other regions enriched with water and choline. These heterogeneities are observed to extend nanometers into the liquid. Additionally, we find that the geranate and geranic acid orient so that their polar carboxyl or carboxylate groups are on average pointed toward the layer containing water and choline. Finally, we report surface tension and thermal expansion coefficients for various concentrations of aqueous CAGE. We find a non-monotonic trend in the surface tension with concentration. The structural and thermodynamic properties we report provide a new perspective on CAGE behavior, which helps deduce the action of CAGE in more sophisticated systems and inspire other studies and applications of CAGE and related materials.

Scope and efficacy of the broad-spectrum topical antiseptic choline geranate.

Choline geranate (also described as Choline And GEranic acid, or CAGE) has been developed as a novel biocompatible antiseptic material capable of penetrating skin and aiding the transdermal delivery of co-administered antibiotics. The antibacterial properties of CAGE were analyzed against 24 and 72 hour old biofilms of 11 clinically isolated ESKAPE pathogens (defined as Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacter sp, respectively), including multidrug resistant (MDR) isolates. CAGE was observed to eradicate in vitro biofilms at concentrations as low as 3.56 mM (0.156% v:v) in as little as 2 hours, which represents both an improved potency and rate of biofilm eradication relative to that reported for most common standard-of-care topical antiseptics in current use. In vitro time-kill studies on 24 hour old Staphylococcus aureus biofilms indicate that CAGE exerts its antibacterial effect upon contact and a 0.1% v:v solution reduced biofilm viability by over three orders of magnitude (a 3log10 reduction) in 15 minutes. Furthermore, disruption of the protective layer of exopolymeric substances in mature biofilms of Staphylococcus aureus by CAGE (0.1% v:v) was observed in 120 minutes. Insight into the mechanism of action of CAGE was provided with molecular modeling studies alongside in vitro antibiofilm assays. The geranate ion and geranic acid components of CAGE are predicted to act in concert to integrate into bacterial membranes, affect membrane thinning and perturb membrane homeostasis. Taken together, our results show that CAGE demonstrates all properties required of an effective topical antiseptic and the data also provides insight into how its observed antibiofilm properties may manifest.

The ionic liquid [C4mpy][Tf2N] induces bound-like structure in the intrinsically disordered protein FlgM.

The A. aeolicus intrinsically disordered protein FlgM has four well-defined α-helices when bound to σ28, but in water FlgM undergoes a change in tertiary structure. In this work, we investigate the structure of FlgM in aqueous solutions of the ionic liquid [C4mpy][Tf2N]. We find that FlgM is induced to fold by the addition of the ionic liquid, achieving average α-helicity values similar to the bound state. Analysis of secondary structure reveals significant similarity with the bound state, but the tertiary structure is found to be more compact. Interestingly, the ionic liquid is not homogeneously dispersed in the water, but instead aggregates near the protein. Separate simulations of aqueous ionic liquid do not show ion clustering, which suggests that FlgM stabilizes ionic liquid aggregation.

From a Liquid to a Crystal without Going through a First-Order Phase Transition: Determining the Free Energy of Melting with Glassy Intermediates.

The excess free energy of a liquid relative to an Einstein crystal reference state is calculated without going through a first-order phase transition. This is accomplished by going through an arrested glassy state to avoid a direct liquid to gas or liquid to crystal transition. The method is demonstrated by calculating the free energy difference between liquid water and ice Ih using the TIP4P and WAIL water models. TIP4P ice Ih melts at 232 ± 1 K, in close agreement with other estimates in the literature. WAIL ice melts at 272 ± 1 K, in good agreement with that of real water, which serves as a good validation of the quality of the WAIL model. The glassy intermediate method is easy to implement and amicable to parallel executions. We expect this method to have broad applications for calculating the liquid excess free energies for other materials.

Hydroxide Solvation and Transport in Anion Exchange Membranes.

Understanding hydroxide solvation and transport in anion exchange membranes (AEMs) can provide important insight into the design principles of these new membranes. To accurately model hydroxide solvation and transport, we developed a new multiscale reactive molecular dynamics model for hydroxide in aqueous solution, which was then subsequently modified for an AEM material. With this model, we investigated the hydroxide solvation structure and transport mechanism in the membrane. We found that a relatively even separation of the rigid side chains produces a continuous overlapping region for hydroxide transport that is made up of the first hydration shell of the tethered cationic groups. Our results show that hydroxide has a significant preference for this overlapping region, transporting through it and between the AEM side chains with substantial contributions from both vehicular (standard diffusion) and Grotthuss (proton hopping) mechanisms. Comparison of the AEM with common proton exchange membranes (PEMs) showed that the excess charge is less delocalized in the AEM than the PEMs, which is correlated with a higher free energy barrier for proton transfer reactions. The vehicular mechanism also contributes considerably more than the Grotthuss mechanism for hydroxide transport in the AEM, while our previous studies of PEM systems showed a larger contribution from the Grotthuss mechanism than the vehicular mechanism for proton transport. The activation energy barrier for hydroxide diffusion in the AEM is greater than that for proton diffusion in PEMs, implying a more significant enhancement of ion transport in the AEM at elevated temperatures.

Influence of the ionic liquid [C4mpy][Tf2N] on the structure of the miniprotein Trp-cage.

We examine the effect of the ionic liquid [C4mpy][Tf2N] on the structure of the miniprotein Trp-cage and contrast these results with the behavior of Trp-cage in water. We find the ionic liquid has a dramatic effect on Trp-cage, though many similarities with aqueous Trp-cage are observed. We assess Trp-cage folding by monitoring root mean square deviation from the crystallographic structure, radius of gyration, proline cis/trans isomerization state, protein secondary structure, amino acid contact formation and distance, and native and non-native contact formation. Starting from an unfolded configuration, Trp-cage folds in water at 298 K in less than 500 ns of simulation, but has very little mobility in the ionic liquid at the same temperature, which can be ascribed to the higher ionic liquid viscosity. At 365 K, the mobility of the ionic liquid is increased and initial stages of Trp-cage folding are observed, however Trp-cage does not reach the native folded state in 2 µs of simulation in the ionic liquid. Therefore, in addition to conventional molecular dynamics, we also employ scaled molecular dynamics to expedite sampling, and we demonstrate that Trp-cage in the ionic liquid does closely approach the aqueous folded state. Interestingly, while the reduced mobility of the ionic liquid is found to restrict Trp-cage motion, the ionic liquid does facilitate proline cis/trans isomerization events that are not seen in our aqueous simulations.

Propensity of Hydrated Excess Protons and Hydroxide Anions for the Air-Water Interface.

Significant effort has been undertaken to better understand the molecular details governing the propensity of ions for the air-water interface. Facilitated by computationally efficient reactive molecular dynamics simulations, new and statistically conclusive molecular-scale results on the affinity of the hydrated excess proton and hydroxide anion for the air-water interface are presented. These simulations capture the dynamic bond breaking and formation processes (charge defect delocalization) that are important for correctly describing the solvation and transport of these complex species. The excess proton is found to be attracted to the interface, which is correlated with a favorable enthalpic contribution and consistent with reducing the disruption in the hydrogen bond network caused by the ion complex. However, a recent refinement of the underlying reactive potential energy function for the hydrated excess proton shows the interfacial attraction to be weaker, albeit nonzero, a result that is consistent with the experimental surface tension measurements. The influence of a weak hydrogen bond donated from water to the protonated oxygen, recently found to play an important role in excess hydrated proton transport in bulk water, is seen to also be important for this study. In contrast, the hydroxide ion is found to be repelled from the air-water interface. This repulsion is characterized by a reduction of the energetically favorable ion-water interactions, which creates an enthalpic penalty as the ion approaches the interface. Finally, we find that the fluctuation in the coordination number around water sheds new light on the observed entropic trends for both ions.

Insights into the transport of aqueous quaternary ammonium cations: a combined experimental and computational study.

This study focuses on understanding the relative effects of ammonium substituent groups (we primarily consider tetramethylammonium, benzyltrimethylammonium, and tetraethylammonium cations) and anion species (OH(-), HCO3(-), CO3(2-), Cl(-), and F(-)) on ion transport by combining experimental and computational approaches. We characterize transport experimentally using ionic conductivity and self-diffusion coefficients measured from NMR. These experimental results are interpreted using simulation methods to describe the transport of these cations and anions considering the effects of the counterion. It is particularly noteworthy that we directly probe cation and anion diffusion with pulsed gradient stimulated echo NMR and molecular dynamics simulations, corroborating these methods and providing a direct link between atomic-resolution simulations and macroscale experiments. By pairing diffusion measurements and simulations with residence times, we were able to understand the interplay between short-time and long-time dynamics with ionic conductivity. With experiment, we determined that solutions of benzyltrimethylammonium hydroxide have the highest ionic conductivity (0.26 S/cm at 65 °C), which appears to be due to differences for the ions in long-time diffusion and short-time water caging. We also examined the effect of CO2 on ionic conductivity in ammonium hydroxide solutions. CO2 readily reacts with OH(-) to form HCO(-)3 and is found to lower the solution ionic conductivity by almost 50%.

Multiscale reactive molecular dynamics.

Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system.

Optimizing the switching function for nonequilibrium free-energy calculations: an on-the-fly approach.

Using nonequilibrium switching simulations to determine the free-energy difference between two thermodynamic states has gained tremendous popularity since Jarzynski's identity was proposed. The efficiency of a nonequilibrium switching simulation depends on the switching function. A well selected switching function can significantly minimize the associated dissipative work and reduce the computational cost of nonequilibrium free-energy simulations. In this paper, a method for estimating an efficient switching function during a nonequilibrium free-energy simulation is presented. The switching rate depends on the fluctuation of the fictitious force and a relaxation time. This method is similar to a prior method described by de Koning [J. Chem. Phys. 122, 104106 (2005)], except in our approach the switching rate is determined on-the-fly without the need for trial pulls. Our method can be easily incorporated into any existing implementation of the nonequilibrium switching method. The on-the-fly approach was used to determine the transformation free energy between two types of Einstein crystals and the isothermal free energy of expansion of a van der Waals gas. For both of the test cases, our on-the-fly method is found to provide a switching function much more superior than the standard one.

Efficient sampling of ice structures by electrostatic switching.

An electrostatic switching procedure is introduced that enables the systematic generation of high-quality ice configurations at various temperatures. Proton disordered ice Ih configurations were generated for the TIP4P water model at temperatures from 50 to 240 K, for the SPC/Fw water model from 100 to 240 K, and for the DC97 water model at 240 K. The resulting configurations were found to properly sample the canonical ensemble. The dielectric constant of ice Ih was determined from the net dipole fluctuation of the ice configurations. The calculated dielectric constant compares favorably with the study by Rick and Haymet [J. Chem. Phys. 2003, 118, 9291]. However, our method gives smaller error bars, especially at lower temperatures. At temperatures above 200 K, a type of hydrogen-bond defect is identified that cannot be categorized as a D or L type defect.

Rapid accumulation of mutations during seed-to-seed propagation of mismatch-repair-defective Arabidopsis.

During the many cell divisions that precede formation of plant gametes, their apical-meristem and floral antecedents are continually exposed to endogenous and environmental mutagenic threats. Although some deleterious recessive mutations may be eliminated during growth of haploid gametophytes and functionally haploid early embryos ("haplosufficiency quality-checking"), the multiplicity of plant genome-maintenance systems suggests aggressive quality control during prior diploid growth. To test in Arabidopsis a hypothesis that prior mismatch repair (MMR) is paramount in defense of plant genetic fidelity, we propagated in parallel 36 MMR-defective (Atmsh2-1) and 36 wild-type lines. The Atmsh2-1 lines rapidly accumulated a wide variety of mutations: fifth-generation (G5) plants showed abnormalities in morphology and development, fertility, germination efficiency, seed/silique development, and seed set. Only two Atmsh2-1, but all 36 wild-type lines, appeared normal at G5. Analyses of insertion/deletion mutation at six repeat-sequence (microsatellite) loci showed each Atmsh2-1 line to have evolved its own "fingerprint," the results of as many as 10 microsatellite mutations in a single line. Thus, MMR during diploid growth is essential for plant genomic integrity.