Co-Assembly of Carbon Nanotube Porins into Biomimetic Peptoid Membranes.

Robust and cost-effective membrane-based separations are essential to solving many global crises, such as the lack of clean water. Even though the current polymer-based membranes are widely used for separations, their performance and precision can be enhanced by using a biomimetic membrane architecture that consists of highly permeable and selective channels embedded in a universal membrane matrix. Researchers have shown that artificial water and ion channels, such as carbon nanotube porins (CNTPs), embedded in lipid membranes can deliver strong separation performance. However, their applications are limited by the relative fragility and low stability of the lipid matrix. In this work, we demonstrate that CNTPs can co-assemble into two dimension (2D) peptoid membrane nanosheets, opening up a way to produce highly programmable synthetic membranes with superior crystallinity and robustness. A combination of molecular dynamics (MD) simulations, Raman spectroscopy, X-ray diffraction (XRD), and atomic force microscopy (AFM) measurements to verify the co-assembly of CNTP and peptoids are used and show that it does not disrupt peptoid monomer packing within the membrane. These results provide a new option for designing affordable artificial membranes and highly robust nanoporous solids.

Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins.

RAS is a signaling protein associated with the cell membrane that is mutated in up to 30% of human cancers. RAS signaling has been proposed to be regulated by dynamic heterogeneity of the cell membrane. Investigating such a mechanism requires near-atomistic detail at macroscopic temporal and spatial scales, which is not possible with conventional computational or experimental techniques. We demonstrate here a multiscale simulation infrastructure that uses machine learning to create a scale-bridging ensemble of over 100,000 simulations of active wild-type KRAS on a complex, asymmetric membrane. Initialized and validated with experimental data (including a new structure of active wild-type KRAS), these simulations represent a substantial advance in the ability to characterize RAS-membrane biology. We report distinctive patterns of local lipid composition that correlate with interfacially promiscuous RAS multimerization. These lipid fingerprints are coupled to RAS dynamics, predicted to influence effector binding, and therefore may be a mechanism for regulating cell signaling cascades.

Anionic Lipids Impact RAS-Binding Site Accessibility and Membrane Binding Affinity of CRAF RBD-CRD.

CRAF activation requires binding to membrane-anchored and active GTP-bound RAS. Whereas its RAS-binding domain (RBD) contains the main binding interface to the RAS G domain, its cysteine-rich domain (CRD) is responsible for association to anionic lipid-rich membranes. Both RAF domains are connected by a short linker, and it remains unclear if the two domains act independently or if one domain can impact the function of the other. Here, we used a combination of coarse-grained and all-atom molecular dynamics simulations of a CRAF RBD-CRD construct to investigate the dynamics of the RBD when it is tethered to CRD that is anchored to a POPC:POPS model membrane. First, we show that the RBD positioning is very dynamic with a preferential localization near the membrane surface. Next, we show that membrane-localized RBD has its RAS-binding interface mostly inaccessible because of its proximity to the membrane. Several positively charged residues in this interface were identified from simulations as important for driving RBD association to the membrane. Surface plasmon resonance (SPR) measurements confirmed that mutations of these RBD residues reduced the liposome partitioning of RBD-CRD. Last, simulations indicated that the presence of RBD near the membrane led to a local enrichment of anionic lipids that could potentially enhance the membrane affinity of the entire RBD-CRD construct. This was supported by SPR measurements that showed stronger liposome partitioning of RBD-CRD relative to CRD alone. These findings thus suggest that the RBD and CRD have synergistic effects on their membrane dynamics, with CRD bringing RBD closer to the membrane that impacts its accessibility to RAS and with RBD causing local anionic lipid enrichment that enhances the overall affinity between the membrane and RBD-CRD. These mechanisms have potential implications on the order of events of the interactions between RAS and CRAF at the membrane.

Ionic Liquids with Symmetric Diether Tails: Bulk and Vacuum-Liquid Interfacial Structures.

The behavior in the bulk and at interfaces of biphilic ionic liquids in which either the cation or anion possesses moderately long alkyl tails is to a significant degree well understood. Less clear is what happens when both the cation and anion possess tails that are not apolar, such as in the case of ether functionalities. The current article discusses the structural characteristics of C2OC2OC2-mim+/C2OC2OC2-OSO3- in the bulk and at the vacuum interface. We find that the vacuum interface affects only the nanometer length scale. This is in contrast to what we have recently found in ( J. Phys. Chem. Lett. , 2016 , 7 ( 19 ), 3785 - -3790 ) for isoelectronic C[8]-mim+/C[8]-OSO3-, where the interface effect is long ranged. Interestingly, ions with the diether tail functionality still favor the tail-outward orientation at the vacuum interface and the bulk phase preserves the alternation between charged networks and tails that is commonly observed for biphilic ionic liquids. However, such alternation is less well-defined and results in a significantly diminished first sharp diffraction peak in the bulk liquid structure function.

Structures of Ionic Liquids Having Both Anionic and Cationic Octyl Tails: Lamellar Vacuum Interface vs Sponge-Like Bulk Order.

Numerous experimental and computational studies have shown that the structure of ionic liquids is significantly influenced by confinement and by interactions with interfaces. The nature of the interface can affect the immediate ordering of cations and anions, changing important rheological characteristics relevant to lubrication. Most studies suggest that such changes are local or short-ranged and that bulk properties are reestablished on a length scale of a few nanometers. The current study focuses on the 1-methyl-3-octylimidazolium octylsulfate ionic liquid for which both the cation and anion have moderate length linear alkyl tails. For this system, we find that the bulk phase is dominated by the very common sponge-like morphology characteristic of many ionic liquids. However, at the vacuum interface, a lamellar structure is observed that is not restricted to the vicinity of the surface but instead extends across the full 9 nm slab of our simulation. We suspect that in reality it could extend significantly beyond this.

Communication: Nanoscale structure of tetradecyltrihexylphosphonium based ionic liquids.

In a recent communication [J. J. Hettige et al., J. Chem. Phys. 140, 111102 (2014)], we investigated the anomalous temperature dependence of the X-ray first sharp diffraction peak (or prepeak) in the tetradecyltrihexylphosphonium bis(trifluoromethylsulfonyl)-amide ionic liquid. Contrary to what was expected and often observed, the first sharp diffraction peak in this system was shown to increase in intensity with increasing temperature. This implies higher intermediate-range periodicity at a higher temperature. Is this counter-intuitive behavior specific to the combination of cation and anion? The current work analyzes the structural behavior of the same cation coupled with six different anions ranging from the small and spherically symmetric Cl(-) to the more structurally complex and charge-diffuse NTf2 (-). In all cases, the same temperature behavior trend for the prepeak is observed independent of anionic nature. We will show that the intensity increase in the prepeak region is associated with the structural behavior of charged liquid subcomponents. Instead, upon a temperature increase, the apolar subcomponents contribute to what would be an expected decrease of prepeak intensity.

Ionic liquids-Conventional solvent mixtures, structurally different but dynamically similar.

In more than one way pure ionic liquids (ILs) can be seen as mixtures. By definition they are comprised of cationic and anionic components and they also possess dual charge and apolar characteristics. We recently uncovered interesting dynamical behavior [Araque et al., J. Phys. Chem. B 119(23), 7015 (2015)] that can be ascribed to this duality. For small neutral solutes local friction can be high in certain regions and much lower in others. It is only reasonable to ask whether this interesting behavior is unique to ILs or is also common in certain conventional solvent mixtures such as dimethylsufoxide/glycerol for which the viscosity can be tuned to be similar. We make the case that the latter scenario is correct and that whereas viscous conventional solvent mixtures are structurally very different from ILs, dynamically they are not. From the perspective of a solute that is small, both ILs and viscous conventional solvent mixtures display frictionally stiff and soft regions associated with cage and jump diffusive regimes. In the case of ILs these are associated with charge-enhanced and charge-depleted liquid regions, whereas in the case of the conventional solvents by the distinct frictional properties of the two components.

Modern Room Temperature Ionic Liquids, a Simple Guide to Understanding Their Structure and How It May Relate to Dynamics.

Modern room temperature ionic liquids are structurally defined by symmetries on different length scales. Polar-apolar alternation defines their nanoscale structural heterogeneity, whereas positive-negative charge alternation defines short length scale order. Much progress has been made in the past few years as it pertains to the theoretical interpretation of X-ray scattering experiments for these liquids. Our group has contributed to the development of theoretical interpretation guidelines for the analysis of their structure function. Perhaps less well developed is our understanding of how transport and dynamics in general couple to the very unique structure of ionic liquids which are often dynamically and structurally heterogeneous. This article attempts to present our most current understanding of ionic liquid structure in general and its coupling to transport and dynamics in minimally technical terms for the benefit of the broadest audience.

Bicontinuity and multiple length scale ordering in triphilic hydrogen-bonding ionic liquids.

Triphilic ionic liquids (containing polar, apolar, and fluorinated components) that can hydrogen bond present a new paradigm in ionic liquid structural morphology. In this study we show that butylammonium pentadecafluorooctanoate and its nonfluorinated analogue butylammonium octanoate form disordered bicontinuous phases where a network of charge alternating hydrogen bonds continuously percolate through the whole liquid. These systems show order on multiple length scales, the largest length scale given by the percolating network. Separation between filaments in the network gives rise to a prepeak or first sharp diffraction peak. In the case of the fluorinated system, shorter range order occurs due to apolar-fluorinated alternation that decorates the surface of each individual filament. The backbone of the filaments is the product of the shortest organized length scale, namely, charge alternating hydrogen bonds. Liquid structure obtained via molecular dynamics simulations is used to compute coherent X-ray scattering intensities, and a full picture of the liquid landscape is developed. A careful mathematical analysis of the simulation data proposed here reveals individual molecular correlations that importantly contribute to each feature of the experimental structure function.

Communication: Anomalous temperature dependence of the intermediate range order in phosphonium ionic liquids.

In a recent article by the Castner and Margulis groups [Faraday Discuss. 154, 133 (2012)], we described in detail the structure of the tetradecyltrihexylphosphonium bis(trifluoromethylsulfonyl)-amide ionic liquid as a function of temperature using X-ray scattering, and theoretical partitions of the computationally derived structure function. Interestingly, and as opposed to the case in most other ionic-liquids, the first sharp diffraction peak or prepeak appears to increase in intensity as temperature is increased. This phenomenon is counter intuitive as one would expect that intermediate range order fades as temperature increases. This Communication shows that a loss of hydrophobic tail organization at higher temperatures is counterbalanced by better organization of polar components giving rise to the increase in intensity of the prepeak.

Structure of 1-alkyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)amide ionic liquids with linear, branched, and cyclic alkyl groups.

X-ray scattering and molecular dynamics simulations have been carried out to investigate structural differences and similarities in the condensed phase between pyrrolidinium-based ionic liquids paired with the bis(trifluoromethylsulfonyl)amide (NTf2(-)) anion where the cationic tail is linear, branched, or cyclic. This is important in light of the charge and polarity type alternations that have recently been shown to be present in the case of liquids with cations of moderately long linear tails. For this study, we have chosen to use the 1-alkyl-1-methylpyrrolidinium, Pyrr(1,n(+)) with n = 5 or 7, as systems with linear tails, 1-(2-ethylhexyl)-1-methylpyrrolidinium, Pyrr(1,EtHx(+)), as a system with a branched tail, and 1-(cyclohexylmethyl)-1-methylpyrrolidinium, Pyrr(1,ChxMe(+)), as a system with a cyclic tail. We put these results into context by comparing these data with recently published results for the Pyrr(1,n(+))/NTf2(-) ionic liquids with n = 4, 6, 8, and 10.1,2 General methods for interpreting the structure function S(q) in terms of q-dependent natural partitionings are described. This allows for an in-depth analysis of the scattering data based on molecular dynamics (MD) trajectories that highlight the effect of modifying the cationic tail.

Anions, the Reporters of Structure in Ionic Liquids.

In this work we compare the role that different anions play in the structure function S(q) for a set of liquids with the same cation. It is well established that because of their amphiphilic nature and their often larger size, cations play a fundamental role in the structural landscape of ionic liquids. On the other hand, it is often atoms in the anions that display the largest X-ray form factors and therefore play a very significant role as reporters of structure in small- and wide-angle X-ray scattering (SAXS/WAXS)-type experiments. For a set of liquids with similar topological landscape, how does S(q) change when the anionic scattering is deemphasized? Also, how do we computationally recover the typical length scale of important and perhaps universal ionic liquid structural features such as charge alternation when these are experimentally inaccessible from S(q) because of interference cancellations? We answer these questions by studying three different tetrapentylammonium-based liquids with the I(-), PF6(-) and N(CN)2(-) anions.

How does the ionic liquid organizational landscape change when nonpolar cationic alkyl groups are replaced by polar isoelectronic diethers?

X-ray scattering experiments and molecular dynamics simulations have been performed to investigate the structure of four room temperature ionic liquids (ILs) comprising the bis(trifluoromethylsulfonyl)amide (NTf(2)(-)) anion paired with the triethyloctylammonium (N(2228)(+)) and triethyloctylphosphonium (P(2228)(+)) cations and their isoelectronic diether analogs, the (2-ethoxyethoxy)ethyltriethylammonium (N(222(2O2O2))(+)) and (2-ethoxyethoxy)ethyltriethylphosphonium (P(222(2O2O2))(+)) cations. Agreement between simulations and experiments is good and permits a clear interpretation of the important topological differences between these systems. The first sharp diffraction peak (or prepeak) in the structure function S(q) that is present in the case of the liquids containing the alkyl-substituted cations is absent in the case of the diether substituted analogs. Using different theoretical partitioning schemes for the X-ray structure function, we show that the prepeak present in the alkyl-substituted ILs arises from polarity alternations between charged groups and nonpolar alkyl tails. In the case of the diether substituted ILs, we find considerable curling of tails. Anions can be found with high probability in two different environments: close to the cationic nitrogen (phosphorus) and also close to the two ether groups. For the two diether systems, anions are found in locations from which they are excluded in the alkyl-substituted systems. This removes the longer range (polar/nonpolar) pattern of alternation that gives rise to the prepeak in alkyl-substituted systems.

SAXS anti-peaks reveal the length-scales of dual positive-negative and polar-apolar ordering in room-temperature ionic liquids.

Structural patterns that have the same spatial periodicity but a phase offset give rise to peaks and anti-peaks (negative-going peaks) at the same q value in the SAXS structure function S(q). As an example, in ionic liquids we often find charge alternation, and at the distance where one finds a density enhancement of charges of the same type one also finds a depletion of charges of opposite sign. Another such situation arises with polar-apolar densities. At distances where there is enhancement of same-type (polar-polar or apolar-apolar) densities there is also a depletion of opposite-type (polar-apolar) density. This gives rise to prepeaks and what we call same spatial periodicity anti-prepeaks.