Water in Nanopores and Biological Channels: A Molecular Simulation Perspective

Molecular mechanism of anion permeation through aquaporin 6

Aquaporins (AQPs) are recognized as transmembrane water channels that facilitate selective water permeation through their monomeric pores. Among the AQP family, AQP6 has an intriguing characteristic as an anion channel, which is allosterically controlled by pH conditions and is eliminated by a single amino acid mutation. However, the molecular mechanism of anion permeation through AQP6 remains unclear. Using molecular dynamics simulations in the presence of a transmembrane voltage utilizing an ion concentration gradient, we show that chloride ions permeate through the pore corresponding to the central axis of the AQP6 homotetramer. Under low pH conditions, a subtle opening of the hydrophobic selectivity filter (SF), located near the extracellular part of the central pore, becomes wetted and enables anion permeation. Our simulations also indicate that a single mutation (N63G) in human AQP6, located at the central pore, significantly reduces anion conduction, consistent with experimental data. Moreover, we demonstrate that the pH-sensing mechanism in which the protonation of H184 and H189 under low pH conditions allosterically triggers the gating of the SF region. These results suggest a unique pH-dependent allosteric anion permeation mechanism in AQP6 and could clarify the role of the central pore in some of the AQP tetramers.

Gas-Responsive and Gas-Releasing Polymer Assemblies

In order to explore the unique physiological roles of gas signaling molecules and gasotransmitters in vivo, chemists have engineered a variety of gas-responsive polymers that can monitor their changes in cellular milieu, and gas-releasing polymers that can orchestrate the release of gases. These have advanced their potential applications in the field of bio-imaging, nanodelivery, and theranostics. Since these polymers are of different chain structures and properties, the morphology of their assemblies will manifest distinct transitions after responding to gas or releasing gas. In this review, we summarize the fundamental design rationale of gas-responsive and gas-releasing polymers in structure and their controlled transition in self-assembled morphology and function, as well as present some perspectives in this prosperous field. Emerging challenges faced for the future research are also discussed.

Electronic Polarization Leads to a Drier Dewetted State for Hydrophobic Gating in the Big Potassium Channel

In the hydrophobic gating mechanism proposed for some ion channels, ion permeation is not blocked by the physical dimension of the channel pore but by its dewetted state which constitutes the energetic bottleneck. A major source of uncertainty in the mechanism is that the dewetted state was not observed in experiments and only probed in simulations using nonpolarizable force fields, which do not accurately represent the properties of confined water. Here we analyze hydration of the central cavity in the pore-gate domain of the Big Potassium channel using molecular dynamics and grand canonical Monte Carlo simulations with enhanced sampling techniques. Including polarization leads to a much drier dewetted state and a higher barrier for the transition to the wet state, suggesting more effective hydrophobic gating. The simulations also identify two backbone carbonyls at the bottom of the selectivity filter as good candidates for characterizing the dewetted state using infrared spectroscopies.

Influence of the Water Model on the Structure and Interactions of the GPR40 Protein with the Lipid Membrane and the Solvent: Rigid versus Flexible Water Models

G protein-coupled receptors (GPCR) are responsible for modulating various physiological functions and are thus related to the pathophysiology of different diseases. Being potential therapeutic targets, multiple computational methodologies have been developed to analyze their behavior and interactions with other species. The solvent, on the other hand, has received much less attention. In this work, we analyzed the effect of four explicit water models on the structure and interactions of the GPR40 receptor in its apo form. We employed the rigid SPC/E and TIP4P models, and their flexible versions, the FBA/ϵ and TIP4P/ϵflex. We explored the structural changes and their correlation with some bulk dynamic properties of water. Our results showed an adverse effect on the conservation of the secondary structure of the receptor with all the models due to the breaking of the intramolecular hydrogen bond network, being more evident for the TIP4P models. Notably, all four models brought the receptor to states similar to the active one, modifying the intracellular part of the TM5 and TM6 domains in a "hinge" type movement, allowing the opening of the structure. Regarding the dynamic properties, the rigid models showed results comparable to those obtained in other studies on membrane systems. However, flexible models exhibit disparities in the molecular representation of systems. Surprisingly, the FBA/ϵ model improves the molecular picture of several properties, even though their agreement with bulk diffusion is poorer. These findings reinforce our idea that exploring other water models or improving the current ones, to better represent the membrane interface, can lead to a positive impact on the description of the signal transduction mechanisms and the search of new drugs by targeting these receptors.

Biosimilars in the Era of Artificial Intelligence-International Regulations and the Use in Oncological Treatments

This research is based on three fundamental aspects of successful biosimilar development in the challenging biopharmaceutical market. First, biosimilar regulations in eight selected countries: Japan, South Korea, the United States, Canada, Brazil, Argentina, Australia, and South Africa, represent the four continents. The regulatory aspects of the countries studied are analyzed, highlighting the challenges facing biosimilars, including their complex approval processes and the need for standardized regulatory guidelines. There is an inconsistency depending on whether the biosimilar is used in a developed or developing country. In the countries observed, biosimilars are considered excellent alternatives to patent-protected biological products for the treatment of chronic diseases. In the second aspect addressed, various analytical AI modeling methods (such as machine learning tools, reinforcement learning, supervised, unsupervised, and deep learning tools) were analyzed to observe patterns that lead to the prevalence of biosimilars used in cancer to model the behaviors of the most prominent active compounds with spectroscopy. Finally, an analysis of the use of active compounds of biosimilars used in cancer and approved by the FDA and EMA was proposed.

Strength, number, and kinetics of hydrogen bonds for water confined inside boron nitride nanotubes

Water has shown a myriad of highly interesting properties and behaviors, such as very low friction, phase transition under unexpected conditions, massive property alterations, etc. inside strong nanoconfinements of few-nanometer to sub-nanometer diameters. Water-water hydrogen bonding is one of the most important factors dictating such water behavior and properties inside such strong nanoconfinements. In this paper, we employ Reactive Force Field (ReaxFF) molecular dynamics (MD) simulations for studying multiple facets of such water-water hydrogen bonds (HBs) inside boron-nitride nanotubes (BNNTs) having diameters ranging from a few nanometers to sub-nanometers. First, the strength of the water-water HB interactions, as a function of the HB configuration, is quantified by studying the corresponding PMF (potential of mean force). For water present in extreme confinements (BNNTs with sub-nanometric diameters), we see completely isolated HB basins. On the other hand, for bulk water the HB basin is connected (via a saddle point) to a nearby second PMF well. Therefore, our analysis successfully distinguishes the HB characteristics between the cases of water in extreme confinement and bulk water. Second, we study the kinetics of such water-water HBs: HBs formed by a given pair of water molecules in extreme confinements show a much larger probability of remaining intact once formed or re-forming after they have been broken. Both these results, which shed new light on water-water hydrogen bonding inside strong nanoconfinements, can be explained by the single-file structure formed by the water molecules in extreme BNNT confinements.

Confinement Effects on Proton Transfer in TiO2 Nanopores from Machine Learning Potential Molecular Dynamics Simulations

Improved understanding of proton transfer in nanopores is critical for a wide range of emerging applications, yet experimentally probing mechanisms and energetics of this process remains a significant challenge. To help reveal details of this process, we developed and applied a machine learning potential derived from first-principles calculations to examine water reactivity and proton transfer in TiO2 slit-pores. We find that confinement of water within pores smaller than 0.5 nm imposes strong and complex effects on water reactivity and proton transfer. Although the proton transfer mechanism is similar to that at a TiO2 interface with bulk water, confinement reduces the activation energy of this process, leading to more frequent proton transfer events. This enhanced proton transfer stems from the contraction of oxygen-oxygen distances dictated by the interplay between confinement and hydrophilic interactions. Our simulations also highlight the importance of the surface topology, where faster proton transport is found in the direction where a unique arrangement of surface oxygens enables the formation of an ordered water chain. In a broader context, our study demonstrates that proton transfer in hydrophilic nanopores can be enhanced by controlling pore size, surface chemistry, and topology.

Effects of Nanoconfinement on Dynamics in Concentrated Aqueous Magnesium Chloride Solutions

Water behavior in various natural and manufactured settings is influenced by confinement in organic or inorganic frameworks and the presence of solutes. Here, the effects on dynamics from both confinement and the addition of solutes are examined. Specifically, water and ion dynamics in concentrated (2.5-4.2 m) aqueous magnesium chloride solutions confined in mesoporous silica (2.8 nm pore diameter) were investigated using polarization selective pump-probe and 2D infrared spectroscopies. Fitting the rotational and spectral diffusion dynamics measured by the vibrational probe, selenocyanate, with a previously developed two-state model revealed distinct behaviors at the interior of the silica pores (core state) and near the wall of the confining framework (shell state). The shell dynamics are noticeably slower than the bulk, or core, dynamics. The concentration-dependent slowing of the dynamics aligns with behavior in the bulk solutions, but the spectrally separated water-associated and Mg2+-associated forms of the selenocyanate probe exhibit different responses to confinement. The disparity in the complete reorientation times is larger upon confinement, but the spectral diffusion dynamics become more similar near the silica surface. The length scales that characterize the transition from surface-influenced to bulk-like behavior for the salt solutions in the pores are discussed and compared to those of pure water and an organic solvent confined in the same pores. These comparisons offer insights into how confinement modulates the properties of different liquids.

Impact of Confinement and Zwitterionic Ligand Chemistry on Ion-Ion Selectivity of Functionalized Nanopores

Membranes incorporating zwitterionic chemistries have recently emerged as promising candidates for facilitating challenging ion-ion separations. Transport of ions in such membranes predominantly occurs in hydrated nanopores lined with zwitterionic monomers. To shed light on the physics of ion-ion selectivity underlying such materials, we conducted molecular dynamics simulations of sodium halide transport in model nanopores grafted with sulfobetaine methacrylate molecules. Our results reveal that in both functionalized and unfunctionalized nanopores smaller ions prefer to reside near the pore center, while the larger ions tend to reside near the pore walls. An enhancement in the selective transport of larger anions is observed within the unfunctionalized nanopores relative to that in salt-in-water solutions. Upon functionalization of the nanopores with zwitterions (ZIs), the disparities in the anionic distribution profiles within the pores coupled with differences in the anion-ZI interactions result in a slowdown of larger anions relative to smaller anions. Increasing the ZI grafting density exacerbates these effects, further promoting the selective transport of smaller anions. Our results suggest that selectivity toward large anions can be realized by using nanoporous membranes with ZI content that is high enough to facilitate ion/water partitioning into the pores while preserving the characteristic tendency of the unfunctionalized pores to facilitate faster transport of the larger anions. On the other hand, selectivity toward smaller anions can be achieved by targeting ZI content within the pores that is high enough to significantly slow down the transport of large anions but not high enough to hinder the partitioning of ions/water molecules into the pore due to steric effects.

Assessing the structural stability and drug encapsulation efficiency of poly(ethylene glycol)-poly(L-lactic acid) nanoparticles loaded with atorvastatin calcium: Based on dissipative particle dynamics

Block polymer micelles have been proven highly biocompatible and effective in improving drug utilization for delivering atorvastatin calcium. Therefore, it is of great significance to measure the stability of drug-loading nano micelles from the perspective of block polymer molecular sequence design, which would provide theoretical guidance for subsequent clinical applications. This study aims to investigate the structural stability of drug-loading micelles formed by two diblock/triblock polymers with various block sequences through coarse-grained dissipative particle dynamics (DPD) simulations. From the perspectives of the binding strength of poly(L-lactic acid) (PLLA) and polyethylene glycol (PEG) in nanoparticles, hydrophilic bead surface coverage, and the morphological alteration of nanoparticles induced by shear force, the ratio of hydrophilic/hydrophobic sequence length has been observed to affect the stability of nanoparticles. We have found that for diblock polymers, PEG3kda-PLLA2kda has the best stability (corresponding hydrophilic coverage ratio is 0.832), while PEG4kda-PLLA5kda has the worst (coverage ratio 0.578). For triblock polymers, PEG4kda-PLLA2kda-PEG4kda has the best stability (0.838), while PEG4kda-PLLA5kda-PEG4kda possesses the worst performance (0.731), and the average performance on stability is better than nanoparticles composed of diblock polymers.

Efficient Sampling of Cavity Hydration in Proteins with Nonequilibrium Grand Canonical Monte Carlo and Polarizable Force Fields

Prediction of the hydration levels of protein cavities and active sites is important to both mechanistic analysis and ligand design. Due to the unique microscopic environment of these buried water molecules, a polarizable model is expected to be crucial for an accurate treatment of protein internal hydration in simulations. Here we adapt a nonequilibrium candidate Monte Carlo approach for conducting grand canonical Monte Carlo simulations with the Drude polarizable force field. The GPU implementation enables the efficient sampling of internal cavity hydration levels in biomolecular systems. We also develop an enhanced sampling approach referred to as B-walking, which satisfies detailed balance and readily combines with grand canonical integration to efficiently calculate quantitative binding free energies of water to protein cavities. Applications of these developments are illustrated in a solvent box and the polar ligand binding site in trypsin. Our simulation results show that including electronic polarization leads to a modest but clear improvement in the description of water position and occupancy compared to the crystal structure. The B-walking approach enhances the range of water sampling in different chemical potential windows and thus improves the accuracy of water binding free energy calculations.

Spontaneous Dipole Reorientation in Confined Water and Its Effect on Wetting/Dewetting of Hydrophobic Nanopores

The properties of nanoconfined fluids are important for a broad range of natural and engineering systems. In particular, wetting/dewetting of hydrophobic nanoporous materials is crucial due to their broad applicability for molecular separation and liquid purification; energy storage, conversion, recuperation, and dissipation; for catalysis, chromatography, and so on. In this work, a rapid, orchestrated, and spontaneous dipole reorientation was observed in hydrophobic nanotubes of various pore sizes d (7.9-16.5 Å) via simulations. This phenomenon leads to the fragmentation of water clusters in the narrow nanopores (d = 7.9, 10 Å) and strongly affects dewetting through cluster repulsion. The cavitation in these pores has an electrostatic origin. The dependence of hydrogen-bonded network properties on the tube aperture is obtained and is used to explain wetting (intrusion)-dewetting (extrusion) hysteresis. Computer simulations and experimental data demonstrate that d equals ca. 12.5 Å is a threshold between a nonhysteretic (spring) behavior, where intrusion-extrusion is reversible, and a hysteretic one (shock absorber), where hysteresis is prominent. This work suggests that water clustering and the electrostatic nature of cavitation are important factors that can be effectively exploited for controlling the wetting/dewetting of nanoporous materials.

Water inside the Selectivity Filter of a K+ Ion Channel: Structural Heterogeneity, Picosecond Dynamics, and Hydrogen Bonding

Water inside biological ion channels regulates the key properties of these proteins, such as selectivity, ion conductance, and gating. In this article, we measure the picosecond spectral diffusion of amide I vibrations of an isotope-labeled KcsA potassium channel using two-dimensional infrared (2D IR) spectroscopy. By combining waiting time (100-2000 fs) 2D IR measurements of the KcsA channel including 13C18O isotope-labeled Val76 and Gly77 residues with molecular dynamics simulations, we elucidated the site-specific dynamics of water and K+ ions inside the selectivity filter of KcsA. We observe inhomogeneous 2D line shapes with extremely slow spectral diffusion. Our simulations quantitatively reproduce the experiments and show that water is the only component with any appreciable dynamics, whereas K+ ions and the protein are essentially static on a picosecond timescale. By analyzing simulated and experimental vibrational frequencies, we find that water in the selectivity filter can be oriented to form hydrogen bonds with adjacent or nonadjacent carbonyl groups with the reorientation timescales being three times slower and comparable to that of water molecules in liquid, respectively. Water molecules can reside in the cavity sufficiently far from carbonyls and behave essentially like "free" gas-phase-like water with fast reorientation times. Remarkably, no interconversion between these configurations was observed on a picosecond timescale. These dynamics are in stark contrast with liquid water, which remains highly dynamic even in the presence of ions at high concentrations.

Unipolar Solution Flow in Calcium-Organic Frameworks for Seawater-Evaporation-Induced Electricity Generation

Seawater-flow- and -evaporation-induced electricity generation holds significant promise in advancing next-generation sustainable energy technologies. This method relies on the electrokinetic effect but faces substantial limitations when operating in a highly ion-concentrated environment, for example, natural seawater. We present herein a novel solution using calcium-based metal-organic frameworks (MOFs, C12H6Ca2O19·2H2O) for seawater-evaporation-induced electricity generation. Remarkably, Ca-MOFs show an open-circuit voltage of 0.4 V and a short-circuit current of 14 μA when immersed in seawater under natural conditions. Our experiments and simulations revealed that sodium (Na) ions selectively transport within sub-nanochannels of these synthetic superhydrophilic MOFs. This selective ion transport engenders a unipolar solution flow, which drives the electricity generation behavior in seawater. This work not only showcases an effective Ca-MOF for electricity generation through seawater flow/evaporation but also contributes significantly to our understanding of water-driven energy harvesting technologies and their potential applications beyond this specific context.

Fluoride Transport and Inhibition Across CLC Transporters

The Chloride Channel (CLC) family includes proton-coupled chloride and fluoride transporters. Despite their similar protein architecture, the former exchange two chloride ions for each proton and are inhibited by fluoride, whereas the latter efficiently transport one fluoride in exchange for one proton. The combination of structural, mutagenesis, and functional experiments with molecular simulations has pinpointed several amino acid changes in the permeation pathway that capitalize on the different chemical properties of chloride and fluoride to fine-tune protein function. Here we summarize recent findings on fluoride inhibition and transport in the two prototypical members of the CLC family, the chloride/proton transporter from Escherichia coli (CLC-ec1) and the fluoride/proton transporter from Enterococcus casseliflavus (CLCF-eca).

Water inside the selectivity filter of a K+ ion channel: structural heterogeneity, picosecond dynamics, and hydrogen-bonding

Water inside biological ion channels regulates the key properties of these proteins such as selectivity, ion conductance, and gating. In this Article we measure the picosecond spectral diffusion of amide I vibrations of an isotope labeled KcsA potassium channel using two-dimensional infrared (2D IR) spectroscopy. By combining waiting time (100 - 2000 fs) 2D IR measurements of the KcsA channel including 13C18O isotope labeled Val76 and Gly77 residues with molecular dynamics simulations, we elucidated the site-specific dynamics of water and K+ ions inside the selectivity filter of KcsA. We observe inhomogeneous 2D lineshapes with extremely slow spectral diffusion. Our simulations quantitatively reproduce the experiments and show that water is the only component with any appreciable dynamics, whereas K+ ions and the protein are essentially static on a picosecond timescale. By analyzing simulated and experimental vibrational frequencies, we find that water in the selectivity filter can be oriented to form hydrogen bonds with adjacent, or non-adjacent carbonyl groups with the reorientation timescales being three times slower and comparable to that of water molecules in liquid, respectively. Water molecules can reside in the cavity sufficiently far from carbonyls and behave essentially like "free" gas-phase-like water with fast reorientation times. Remarkably, no interconversion between these configurations were observed on a picosecond timescale. These dynamics are in stark contrast with liquid water that remains highly dynamic even in the presence of ions at high concentrations.

Structure and Dynamics of Confined Water Inside Diphenylalanine Peptide Nanotubes

Diphenylalanine (FF) peptides exhibit a unique ability to self-assemble into nanotubes with confined water molecules playing pivotal roles in their structure and function. This study investigates the structure and dynamics of diphenylalanine peptide nanotubes (FFPNTs) using all-atom molecular dynamics (MD) and grand canonical Monte Carlo combined with MD (GCMC/MD) simulations with both the CHARMM additive and Drude polarizable force fields. The occupancy and dynamics of confined water molecules were also examined. It was found that less than 2 confined water molecules per FF help stabilize the FFPNTs on the x-y plane. Analyses of the kinetics of confined water molecules revealed distinctive transport behaviors for bound and free water, and their respective diffusion coefficients were compared. Our results validate the importance of polarizable force field models in studying peptide nanotubes and provide insights into our understanding of nanoconfined water.

Hydrophobic gating in bundle-crossing ion channels: a case study of TRPV4

Transmembrane ion channels frequently regulate ion permeation by forming bundle crossing of the pore-lining helices when deactivated. The resulting physical constriction is believed to serve as the de facto gate that imposes the major free energy barrier to ion permeation. Intriguingly, many ion channels also contain highly hydrophobic inner pores enclosed by bundle crossing, which can undergo spontaneous dewetting and give rise to a "vapor barrier" to block ion flow even in the absence of physical constriction. Using atomistic simulations, we show that hydrophobic gating and bundle-crossing mechanisms co-exist and complement one and another in the human TRPV4 channel. In particular, a single hydrophilic mutation in the lower pore can increase pore hydration and reduce the ion permeation free energy barrier by about half without affecting the bundle crossing. We believe that hydrophobic gating may play a key role in other bundle-crossing ion channels with hydrophobic inner pores.

Sequence similarity network and protein structure prediction offer insights into the evolution of microbial pathways for ferrous iron oxidation

IMPORTANCE

Microbial Fe(II) oxidation is a crucial process that harnesses and converts the energy available in Fe, contributing significantly to global element cycling. However, there are still many aspects of this process that remain unexplored. In this study, we utilized a combination of comparative genomics, sequence similarity network analysis, and artificial intelligence-driven structure modeling methods to address the lack of structural information on Fe(II) oxidation proteins and offer a comprehensive perspective on the evolution of Fe(II) oxidation pathways. Our findings suggest that several microbial Fe(II) oxidation pathways currently known may have originated within classes Gammaproteobacteria and Betaproteobacteria.

Sponge-phase Lipid Droplets as Synthetic Organelles: An Ultrafast Study of Hydrogen Bonding and Interfacial Environments

Bottom-up design of biomimetic organelles has gained recent attention as a route towards understanding the transition between non-living matter and life. Despite various artificial lipid membranes being developed, the specific relations between lipid structure, composition, interfacial properties, and morphology are not currently understood. Sponge-phase droplets contain dense, nonlamellar lipid bilayer networks that capture the complexities of the endoplasmic reticulum (ER), making them ideal artificial models of such organelles. Here, we combine ultrafast two-dimensional infrared (2D IR) spectroscopy and molecular dynamics simulations to investigate the interfacial H-bond networks in sponge-phase droplets composed of glycolipid and nonionic detergents. In the sponge phase, the interfacial environments are more hydrated and water molecules confined to the nanometer-scale aqueous channels in the sponge phase exhibit dynamics that are significantly slower compared to bulk water. Surfactant configurations and microscopic phase separation play a dominant role in determining membrane curvature and slow dynamics observed in the sponge phase. The studies suggest that H-bond networks within the nanometer-scale channels are disrupted not only by confinement but also by the interactions of surfactants, which extend 1-2 nm from the bilayer surface. The results provide a molecular-level description for controlling phase and morphology in the design of synthetic lipid organelles.

Hydrophobin Bilayer as Water Impermeable Protein Membrane

One of the most important properties of membranes is their permeability to water and other small molecules. A targeted change in permeability allows the passage of molecules to be controlled. Vesicles made of membranes with low water permeability are preferable for drug delivery, for example, because they are more stable and maintain the drug concentration inside. This study reports on the very low water permeability of pure protein membranes composed of a bilayer of the amphiphilic protein hydrophobin HFBI. Using a droplet interface bilayer setup, we demonstrate that HFBI bilayers are essentially impermeable to water. HFBI bilayers withstand far larger osmotic pressures than lipid membranes. Only by disturbing the packing of the proteins in the HFBI bilayer is a measurable water permeability induced. To investigate possible molecular mechanisms causing the near-zero permeability, we used all-atom molecular dynamics simulations of various HFBI bilayer models. The simulations suggest that the experimental HFBI bilayer permeability is compatible neither with a lateral honeycomb structure, as found for HFBI monolayers, nor with a residual oil layer within the bilayer or with a disordered lateral packing similar to the packing in lipid bilayers. These results suggest that the low permeabilities of HFBI and lipid bilayers rely on different mechanisms. With their extremely low but adaptable permeability and high stability, HFBI membranes could be used as an osmotic pressure-insensitive barrier in situations where lipid membranes fail such as desalination membranes.

Assessment of an Electrostatic Energy-Based Charge Model for Modeling the Electrostatic Interactions in Water Solvent

The protein force field based on the restrained electrostatic potential (RESP) charges has limitations in accurately describing hydrogen bonding interactions in proteins. To address this issue, we propose an alternative approach called the electrostatic energy-based charges (EEC) model, which shows improved performance in describing electrostatic interactions (EIs) of hydrogen bonds in proteins. In this study, we further investigate the performance of the EEC model in modeling EIs in water solvent. Our findings demonstrate that the fixed EEC model can effectively reproduce the quantum mechanics/molecular mechanics (QM/MM)-calculated EIs between a water molecule and various water solvent environments. However, to achieve the same level of computational accuracy, the electrostatic potential (ESP) charge model needs to fluctuate according to the electrostatic environment. Our analysis indicates that the requirement for charge adjustments depends on the specific mathematical and physical representation of EIs as a function of the environment for deriving charges. By comparing with widely used empirical water models calibrated to reproduce experimental properties, we confirm that the performance of the EEC model in reproducing QM/MM EIs is similar to that of general purpose TIP4P-like water models such as TIP4P-Ew and TIP4P/2005. When comparing the computed 10,000 distinct EI values within the range of -40 to 0 kcal/mol with the QM/MM results calculated at the MP2/aug-cc-pVQZ/TIP3P level, we noticed that the mean unsigned error (MUE) for the EEC model is merely 0.487 kcal/mol, which is remarkably similar to the MUE values of the TIP4P-Ew (0.63 kcal/mol) and TIP4P/2005 (0.579 kcal/mol) models. However, both the RESP method and the TIP3P model exhibit a tendency to overestimate the EIs, as evidenced by their higher MUE values of 1.761 and 1.293 kcal/mol, respectively. EEC-based molecular dynamics simulations have demonstrated that, when combined with appropriate van der Waals parameters, the EEC model can closely reproduce oxygen-oxygen radial distribution function and density of water, showing a remarkable similarity to the well-established TIP4P-like empirical water models. Our results demonstrate that the EEC model has the potential to build force fields with comparable accuracy to more sophisticated empirical TIP4P-like water models.

Unravelling Ultrafast Li Ion Transport in Functionalized Metal-Organic Framework-Based Battery Electrolytes

Nonaqueous fluidic transport and ion solvation properties under nanoscale confinement are poorly understood, especially in ion conduction for energy storage and conversion systems. Herein, metal-organic frameworks (MOFs) and aprotic electrolytes are studied as a robust platform for molecular-level insights into electrolyte behaviors in confined spaces. By employing computer simulations, along with spectroscopic and electrochemical measurements, we demonstrate several phenomena that deviate from the bulk, including modulated solvent molecular configurations, aggregated solvation structures, and tunable transport mechanisms from quasi-solid to quasi-liquid in functionalized MOFs. Technologically, taking advantage of confinement effects may prove useful for addressing stability concerns associated with volatile organic electrolytes while simultaneously endowing ultrafast transport of solvates, resulting in improved battery performance, even at extreme temperatures. The molecular-level insights presented here further our understanding of structure-property relationships of complex fluids at the nanoscale, information that can be exploited for the predictive design of more efficient electrochemical systems.

Confined water-encapsulated activated carbon for capturing short-chain perfluoroalkyl and polyfluoroalkyl substances from drinking water

The global ecological crisis of perfluoroalkyl and polyfluoroalkyl substances (PFASs) in drinking water has gradually shifted from long-chain to short-chain PFASs; however, the widespread established PFAS adsorption technology cannot cope with the impact of such hydrophilic pollutants given the inherent defects of solid-liquid mass transfer. Herein, we describe a reagent-free and low-cost strategy to reduce the energy state of short-chain PFASs in hydrophobic nanopores by employing an in situ constructed confined water structure in activated carbon (AC). Through direct (driving force) and indirect (assisted slip) effects, the confined water introduced a dual-drive mode in the confined water-encapsulated activated carbon (CW-AC) and completely eliminated the mass transfer barrier (3.27 to 5.66 kcal/mol), which caused the CW-AC to exhibit the highest adsorption capacity for various short-chain PFASs (C-F number: 3-6) among parent AC and other adsorbents reported. Meanwhile, benefiting from the chain length- and functional group-dependent confined water-binding pattern, the affinity of the CW-AC surpassed the traditional hydrophobicity dominance and shifted toward hydrophilic short-chain PFASs that easily escaped treatment. Importantly, the ability of CW-AC functionality to directly transfer to existing adsorption devices was verified, which could treat 21,000 bed volumes of environment-related high-load (~350 ng/L short-chain PFAS each) real drinking water to below the World Health Organization's standard. Overall, our results provide a green and cost-effective in situ upgrade scheme for existing adsorption devices to address the short-chain PFAS crisis.

Transient water wires mediate selective proton transport in designed channel proteins

Selective proton transport through proteins is essential for forming and using proton gradients in cells. Protons are conducted along hydrogen-bonded 'wires' of water molecules and polar side chains, which, somewhat surprisingly, are often interrupted by dry apolar stretches in the conduction pathways, inferred from static protein structures. Here we hypothesize that protons are conducted through such dry spots by forming transient water wires, often highly correlated with the presence of the excess protons in the water wire. To test this hypothesis, we performed molecular dynamics simulations to design transmembrane channels with stable water pockets interspersed by apolar segments capable of forming flickering water wires. The minimalist designed channels conduct protons at rates similar to viral proton channels, and they are at least 106-fold more selective for H+ over Na+. These studies inform the mechanisms of biological proton conduction and the principles for engineering proton-conductive materials.

Parallel Implementation of Nonadditive Gaussian Process Potentials for Monte Carlo Simulations

A strategy is presented to implement Gaussian process potentials in molecular simulations through parallel programming. Attention is focused on the three-body nonadditive energy, though all algorithms extend straightforwardly to the additive energy. The method to distribute pairs and triplets between processes is general to all potentials. Results are presented for a simulation box of argon, including full box and atom displacement calculations, which are relevant to Monte Carlo simulation. Data on speed-up are presented for up to 120 processes across four nodes. A 4-fold speed-up is observed over five processes, extending to 20-fold over 40 processes and 30-fold over 120 processes.

Mechanism of Water Intrusion into Flexible ZIF-8: Liquid Is Not Vapor

Zeolitic Imidazolate Frameworks (ZIF) find application in storage and dissipation of mechanical energy. Their distinctive properties linked to their (sub)nanometer size and hydrophobicity allow for water intrusion only under high hydrostatic pressure. Here we focus on the popular ZIF-8 material investigating the intrusion mechanism in its nanoscale cages, which is the key to its rational exploitation in target applications. In this work, we used a joint experimental/theoretical approach combining in operando synchrotron experiments during high-pressure intrusion experiments, molecular dynamics simulations, and stochastic models to reveal that water intrusion into ZIF-8 occurs by a cascade filling of connected cages rather than a condensation process as previously assumed. The reported results allowed us to establish structure/function relations in this prototypical microporous material, representing an important step to devise design rules to synthesize porous media.

Wetting hysteresis induces effective unidirectional water transport through a fluctuating nanochannel

We propose a water pump that actively transports water molecules through nanochannels. Spatially asymmetric noise fluctuations imposed on the channel radius cause unidirectional water flow without osmotic pressure, which can be attributed to hysteresis in the cyclic transition between the wetting/drying states. We show that the water transport depends on fluctuations, such as white, Brownian, and pink noises. Because of the high-frequency components in white noise, fast switching of open and closed states inhibits channel wetting. Conversely, pink and Brownian noises generate high-pass filtered net flow. Brownian fluctuation leads to a faster water transport rate, whereas pink noise has a higher capability to overcome pressure differences in the opposite direction. A trade-off relationship exists between the resonant frequency of the fluctuation and the flow amplification. The proposed pump can be considered as an analogy for the reversed Carnot cycle, which is the upper limit of the energy conversion efficiency.

Unexpected Behavior in Thermal Conductivity of Confined Monolayer Water

Monolayer water can be formed under extreme confinement and will present distinctive thermodynamic properties compared with bulk water. In this work, we perform molecular dynamics simulations to study the thermal conductivity of monolayer water confined in graphene channels, finding an unexpected way of thermal conductivity of monolayer water dependent on its number density, which has a close correlation with the structure of water. The monolayer water is in an amorphous state, and its thermal conductivity increases linearly with the area density when the water density is low at first. Then, the thermal conductivity increases as the number density of water rises, which is attributed to the formation of a crystal structure and the reduction of crystal defects as the number of water molecules increases. After reaching the zenith, the thermal conductivity decreases rapidly owing to the formation of a wrinkle structure of monolayer water with excessive water molecules, which weakens the phonon dispersion. Moreover, we further investigate the remarkable effects of the channel height on both the structure and thermal conductivity of monolayer water. In summary, this study demonstrates the close connection between the thermal conductivity of monolayer water and its structure, contributing to not only expanding the understanding of the thermodynamic property of nanoconfined water but also benefiting the engineering applications for nanofluidics.

Central cavity dehydration as a gating mechanism of potassium channels

The hydrophobic gating model, in which ion permeation is inhibited by the hydrophobicity, rather than a physical occlusion of the nanopore, functions in various ion channels including potassium channels. Available research focused on the energy barriers for ion/water conduction due to the hydrophobicity, whereas how hydrophobic gating affects the function and structure of channels remains unclear. Here, we use potassium channels as examples and conduct molecular dynamics simulations to investigate this problem. Our simulations find channel activities (ion currents) highly correlated with cavity hydration level, implying insufficient hydration as a barrier for ion permeation. Enforced cavity dehydration successfully induces conformational transitions between known channel states, further implying cavity dewetting as a key step in the gating procedure of potassium channels utilizing different activation mechanisms. Our work reveals how the cavity dewetting is coupled to structural changes of potassium channels and how it affects channel activity. The conclusion may also apply to other ion channels.

Spin-lattice relaxation time in water/graphene-oxide dispersion

We present the results of the calculations of the spin-lattice relaxation time of water in contact with graphene oxide by means of all-atom molecular dynamics simulations. We fully characterized the water-graphene oxide interaction through the calculation of the relaxation properties of bulk water and of the contact angle as a function of graphene oxide oxidation state and comparing them with the available experimental data. We then extended the calculation to investigate how graphene oxide alters the dynamical and relaxation properties of water in different conditions and concentrations. We show that, despite the diamagnetic nature of the graphene oxide, the confining effects of the bilayers strongly affect the longitudinal relaxation properties of interfacial water, which presents a reduced dynamics due to hydrogen bonds with oxygen groups on graphene oxide. This property makes graphene oxide an interesting platform to investigate water dynamics in confined geometries and an alternative contrast-agent for magnetic resonance imaging applications, especially in view of the possibility to functionalize graphene oxide from theranostic perspectives.

Different effects of two Poloxamers (L61 and F68) on the conductance of bilayer lipid membranes

The integral conductance of planar lipid bilayer membranes in the presence of two Poloxamers (Pluronics) L61 and F68 with the same lengths of hydrophobic poly(propylene oxide) blocks and the different lengths of hydrophilic poly(ethylene oxide) blocks increases with an increase in the concentration of both Pluronics; however, the shape of the conductance-concentration curves is super linear for L61 and sublinear for F68. In the presence of both Pluronics, rare discrete current jumps are observed against the background of continuous current. At high concentrations, the I-V curves of membranes with both L61 and F68 became nonlinear at sufficiently low voltages but differed significantly. At voltages greater than 50 mV, the conductance of membranes with L61 increased sharply and quantized jumps were observed toward higher conductance, which could be interpreted as the appearance of additional pores. On the contrary, the conductance of membranes with F68 decreased and quantized jumps to lower conductance were observed, which could be interpreted as blocking of already existing pores. We attributed the differences in the conductance-concentration and I-V curves of these two Pluronics to their different effects on the dynamics of membrane hydration and, accordingly, on the probability of formation of conducting pores.

Conformational Dynamics of Loop L3 in OmpF: Implications toward Antibiotic Translocation and Voltage Gating

In the present work, we delineate the molecular mechanism of a bulky antibiotic permeating through a bacterial channel and uncover the role of conformational dynamics of the constriction loop in this process. Using the temperature accelerated sliced sampling approach, we shed light onto the dynamics of the L3 loop, in particular the F118 to S125 segment, at the constriction regions of the OmpF porin. We complement the findings with single channel electrophysiology experiments and applied-field simulations, and we demonstrate the role of hydrogen-bond stabilization in the conformational dynamics of the L3 loop. A molecular mechanism of permeation is put forward wherein charged antibiotics perturb the network of stabilizing hydrogen-bond interactions and induce conformational changes in the L3 segment, thereby aiding the accommodation and permeation of bulky antibiotic molecules across the constriction region. We complement the findings with single channel electrophysiology experiments and demonstrate the importance of the hydrogen-bond stabilization in the conformational dynamics of the L3 loop. The generality of the present observations and experimental results regarding the L3 dynamics enables us to identify this L3 segment as the source of gating. We propose a mechanism of OmpF gating that is in agreement with previous experimental data that showed the noninfluence of cysteine double mutants that tethered the L3 tip to the barrel wall on the OmpF gating behavior. The presence of similar loop stabilization networks in porins of other clinically relevant pathogens suggests that the conformational dynamics of the constriction loop is possibly of general importance in the context of antibiotic permeation through porins.

Dynamics of Aqueous Electrolyte Solutions: Challenges for Simulations

This Perspective article focuses on recent simulation work on the dynamics of aqueous electrolytes. It is well-established that full-charge, nonpolarizable models for water and ions generally predict solution dynamics that are too slow in comparison to experiments. Models with reduced (scaled) charges do better for solution diffusivities and viscosities but encounter issues describing other dynamic phenomena such as nucleation rates of crystals from solution. Polarizable models show promise, especially when appropriately parametrized, but may still miss important physical effects such as charge transfer. First-principles calculations are starting to emerge for these properties that are in principle able to capture polarization, charge transfer, and chemical transformations in solution. While direct ab initio simulations are still too slow for simulations of large systems over long time scales, machine-learning models trained on appropriate first-principles data show significant promise for accurate and transferable modeling of electrolyte solution dynamics.

Predictive Molecular Models for Charged Materials Systems: From Energy Materials to Biomacromolecules

Electrostatic interactions play a dominant role in charged materials systems. Understanding the complex correlation between macroscopic properties with microscopic structures is of critical importance to develop rational design strategies for advanced materials. But the complexity of this challenging task is augmented by interfaces present in the charged materials systems, such as electrode-electrolyte interfaces or biological membranes. Over the last decades, predictive molecular simulations that are founded in fundamental physics and optimized for charged interfacial systems have proven their value in providing molecular understanding of physicochemical properties and functional mechanisms for diverse materials. Novel design strategies utilizing predictive models have been suggested as promising route for the rational design of materials with tailored properties. Here, an overview of recent advances in the understanding of charged interfacial systems aided by predictive molecular simulations is presented. Focusing on three types of charged interfaces found in energy materials and biomacromolecules, how the molecular models characterize ion structure, charge transport, morphology relation to the environment, and the thermodynamics/kinetics of molecular binding at the interfaces is discussed. The critical analysis brings two prominent field of energy materials and biological science under common perspective, to stimulate crossover in both research field that have been largely separated.

Confinement Effects on Distribution and Transport of Neutral Solutes in a Small Hydrophobic Nanopore

Molecular dynamics simulations are used to study confinement effects in small cylindrical silica pores with extended hydrophobic surface functionalization as realized, for example, in reversed-phase liquid chromatography (RPLC) columns. In particular, we use a 6 nm cylindrical and a 10 nm slit pore bearing the same C₁₈ stationary phase to compare the conditions inside the smaller-than-average pores within an RPLC column to column-averaged properties. Two small, neutral, apolar to moderately polar solutes are used to assess the consequences of spatial confinement for typical RPLC analytes with water (W)-acetonitrile (ACN) mobile phases at W/ACN ratios between 70/30 and 10/90 (v/v). The simulated data show that true bulk liquid behavior, as observed over an extended center region in the 10 nm slit pore, is not recovered within the 6 nm cylindrical pore. Instead, the ACN-enriched solvent layer around the C₁₈ chain ends (the ACN ditch), a general feature of hydrophobic interfaces equilibrated with aqueous-organic liquids, extends over the entire pore lumen of the small cylindrical pore. This renders the entire pore a highly hydrophobic environment, where, contrary to column-averaged behavior, neither the local nor the pore-averaged sorption and diffusion of analytes scales directly with the W/ACN ratio of the mobile phase. Additionally, the solute polarity-related discrimination between analytes is enhanced. The consequences of local ACN ditch overlap in RPLC columns are reminiscent of ion transport in porous media with charged surfaces, where electrical double-layer overlap occurring locally in smaller pores leads to discrimination between co- and counterionic species.

Proton Configuration in Water Chain on Pt(533)

In this paper, a wetting behavior of Pt(533) is studied by using heterodyne-detected vibrational sum-frequency generation spectroscopy under an ultrahigh-vacuum condition at 145 K. The imaginary parts of the surface nonlinear susceptibility (Imχ⁽²⁾) of the H-bonded OH stretching region are successfully obtained for submonolayer water coverage that show negative bands indicating H-down (proton pointing to the substrate) configurations both for the water at the step and at the terrace. The growth manner of the Imχ⁽²⁾ signal with coverage and the results of an isotopic dilution are consistent with a model in which a one-dimensional (1D) chain at the step forms a "zigzag" structure that contains H-down orientations. This finding resolves the previous controversy in the literature concerning the proton configuration in the 1D water chain at the step.

Dynamics of a colloid-in-tube host-guest system

Originated from supramolecular chemistry, the host-guest concept is generalized and appreciated across the fields of enzyme catalysis, biological channel conduction, and carbon nanotube transport, to name a few. Despite the extensive study of host-guest thermodynamics, it is still a fundamental challenge to directly measure its dynamics in real-space and real-time. Herein we approach such dynamics by direct imaging and tracking in a colloid-in-tube system, where self-assembled tubes are the hosts and sphere particles are the guests. The key difference from a previously reported static 1D confinement is that the present tubes are thermally actuated and capable of translations and rotations. It is the host tube thermal motions that impose a number of anomalies to guest particle dynamics including broadened distribution perpendicular to the tube, enhanced diffusion parallel to the tube phenomenologically resembling the rapid flow in ion channels or carbon nanotubes, and induced long-range particle-particle attraction analogous to capillary condensation. This work in the colloidal system is of wide implications for host-guest systems that are naturally embedded in thermal fluctuations such as transmembrane ion channels and carbon nanotube arrays in a soft matrix.

Effect of the Topology on Wetting and Drying of Hydrophobic Porous Materials

Establishing molecular mechanisms of wetting and drying of hydrophobic porous materials is a general problem for science and technology within the subcategories of the theory of liquids, chromatography, nanofluidics, energy storage, recuperation, and dissipation. In this article, we demonstrate a new way to tackle this problem by exploring the effect of the topology of pure silica nanoparticles, nanotubes, and zeolites. Using molecular dynamics simulations, we show how secondary porosity promotes the intrusion of water into micropores and affects the hydrophobicity of materials. It is demonstrated herein that for nano-objects, the hydrophobicity can be controlled by changing the ratio of open to closed nanometer-sized lateral pores. This effect can be exploited to produce new materials for practical applications when the hydrophobicity needs to be regulated without significantly changing the chemistry or structure of the materials. Based on these simulations and theoretical considerations, for pure silica zeolites, we examined and then classified the experimental database of intrusion pressures, thus leading to the prediction of any zeolite's intrusion pressure. We show a correlation between the intrusion pressure and the ratio of the accessible pore surface area to total pore volume. The correlation is valid for some zeolites and mesoporous materials. It can facilitate choosing prospective candidates for further investigation and possible exploitation, especially for energy storage, recuperation, and dissipation.

Machine learning for non-additive intermolecular potentials: quantum chemistry to first-principles predictions

Prediction of thermophysical properties from molecular principles requires accurate potential energy surfaces (PES). We present a widely-applicable method to produce first-principles PES from quantum chemistry calculations. Our approach accurately interpolates three-body non-additive interaction data, using the machine learning technique, Gaussian Processes (GP). The GP approach needs no bespoke modification when the number or type of molecules is changed. Our method produces highly accurate interpolation from significantly fewer training points than typical approaches, meaning ab initio calculations can be performed at higher accuracy. As an exemplar we compute the PES for all three-body cross interactions for CO₂-Ar mixtures. From these we calculate the CO₂-Ar virial coefficients up to 5th order. The resulting virial equation of state (EoS) is convergent for densities up to the critical density. Where convergent, the EoS makes accurate first-principles predictions for a range of thermophysical properties for CO₂-Ar mixtures, including the compressibility factor, speed of sound and Joule-Thomson coefficient. Our method has great potential to make wide-ranging first-principles predictions for mixtures of comparably sized molecules. Such predictions can replace the need for expensive, laborious and repetitive experiments and inform the continuum models required for applications.

Atomistic Simulation of Molecules Interacting with Biological Nanopores: From Current Understanding to Future Directions

Biological nanopores have been at the focus of numerous studies due to their role in many biological processes as well as their (prospective) technological applications. Among many other topics, recent studies on nanopores have addressed two key areas: antibiotic permeation through bacterial channels and sensing of analytes. Although the two areas are quite far apart in terms of their objectives, in both cases atomistic simulations attempt to understand the solute dynamics and the solute-protein interactions within the channel lumen. While decades of studies on various channels have culminated in an improved understanding of the key molecular factors and led to practical applications in some cases, successful utilization is limited. In this Perspective we summarize recent progress in understanding key issues in molecular simulations of antibiotic translocation and in the development of nanopore sensors. Moreover, we comment on possible advancements in computational algorithms that can potentially resolve some of the issues.