The 50 most-cited articles in The Journal of Physical Chemistry B, 2018

Abstract We demonstrate that Li+ hopping conduction, which cannot be explained by conventional models i.e., Onsager’s theory and Stokes’ law, emerges in highly concentrated liquid electrolytes composed of LiBF4 and sulfolane (SL). Self-diffusion coefficients of Li+ (DLi), BF4– (DBF4), and SL (DSL) were measured with pulsed-field gradient NMR. In the concentrated electrolytes with molar ratios of SL/LiBF4 ≤ 3, the ratios DSL/DLi and DBF4/DLi become lower than 1, suggesting faster diffusion of Li+ than SL and BF4–, and thus the evolution of Li+ hopping conduction. X-ray crystallographic analysis of the LiBF4/SL (1:1) solvate revealed that the two oxygen atoms of the sulfone group are involved in the bridging coordination of two different Li+ ions. In addition, the BF4– anion also participates in the bridging coordination of Li+. The Raman spectra of the highly concentrated LiBF4–SL solution suggested that Li+ ions are bridged by SL and BF4– even in the liquid state. Moreover, detailed investigation along with molecular dynamics simulations suggests that Li+ exchanges ligands (SL and…

Computationally modeling changes in binding free energies upon mutation (interface ΔΔ G) allows large-scale prediction and perturbation of protein-protein interactions. Additionally, methods that consider and sample relevant conformational plasticity should be able to achieve higher prediction accuracy over methods that do not. To test this hypothesis, we developed a method within the Rosetta macromolecular modeling suite (flex ddG) that samples conformational diversity using "backrub" to generate an ensemble of models and then applies torsion minimization, side chain repacking, and averaging across this ensemble to estimate interface ΔΔ G values. We tested our method on a curated benchmark set of 1240 mutants, and found the method outperformed existing methods that sampled conformational space to a lesser degree. We observed considerable improvements with flex ddG over existing methods on the subset of small side chain to large side chain mutations, as well as for multiple simultaneous non-alanine mutations, stabilizing mutations, and mutations in antibody-antigen interfaces.…

We present a general thermodynamic top-down analysis of the effects of oxidants and pH on dopamine oxidation and cyclization, supplemented with UV-vis and electrochemical studies. The model is applicable to other catecholamines and various experimental conditions. The results show that the decisive physicochemical parameters in autoxidation are the p K values of the semiquinone and the amino group in the oxidized quinone. Addition of Ce(IV) or Fe(III) enhances dopamine oxidation in acidic media in aerobic and anaerobic conditions by the direct oxidation of dopamine and, in the presence of oxygen, also by the autoxidation of the formed semiquinone. At pH 4.5, the enhancement of the one-electron oxidation of dopamine explains the overall reaction enhancement, but at a lower pH, cyclization becomes rate-determining. Oxidation by Cu(II) at reasonable rates requires the presence of oxygen or chloride ions.

Deep eutectic solvents (DES) are a class of solvents frequently composed of choline chloride and a neutral hydrogen bond donor (HBD) at ratios of 1:1, 1:2, or 1:3, respectively. As cost-effective and eco-friendly solvents, DESs have gained considerable popularity in multiple fields, including materials, separations, and nanotechnology. In the present work, a comprehensive set of transferable parameters have been fine-tuned to accurately reproduce bulk-phase physical properties and local intermolecular interactions for 8 different choline chloride-based DESs. This nonpolarizable force field, OPLS-DES, gave near quantitative agreement at multiple temperatures for experimental densities, viscosities, heat capacities, and surface tensions yielding overall mean absolute errors (MAEs) of ca. 1.1%, 1.6%, 5.5%, and 1.5%, respectively. Local interactions and solvent structuring between the ions and HBDs, including urea, glycerol, phenol, ethylene glycol, levulinic acid, oxalic acid, and malonic acid, were accurately reproduced when compared to radial distribution functions and coordination…

Here, we show how dynamic nuclear polarization (DNP) NMR spectroscopy experiments permit the atomic level structural characterization of loaded and empty lipid nanoparticles (LNPs). The LNPs used here were synthesized by the microfluidic mixing technique and are composed of ionizable cationic lipid (DLin-MC3-DMA), a phospholipid (distearoylphosphatidylcholine, DSPC), cholesterol, and poly(ethylene glycol) (PEG) (dimyristoyl phosphatidyl ethanolamine (DMPE)–PEG 2000), as well as encapsulated cargoes that are either phosphorothioated siRNA (50 or 100%) or mRNA. We show that LNPs form physically stable complexes with bioactive drug siRNA for a period of 94 days. Relayed DNP experiments are performed to study 1 H– 1 H spin diffusion and to determine the spatial location of the various components of the LNP by studying the average enhancement factors as a function of polarization time. We observe a striking feature of LNPs in the presence and in the absence of encapsulating siRNA or mRNA by comparing our experimental results to numerical spin-diffusion modeling. We observe that LNPs form…

Bioelectronic materials interface biomolecules, cells, organs, or organisms with electronic devices, and they represent an active and growing field of materials research. Protein and peptide nanostructures are ideal bioelectronic materials. They possess many of the properties required for biocompatibility across scales from enzymatic to organismal interfaces, and recent examples of supramolecular protein and peptide nanostructures exhibit impressive electronic properties. The ability of such natural and synthetic protein and peptide materials to conduct electricity over micrometer to centimeter length scales, however, is not readily understood from a conventional view of their amino acid building blocks. Distinct in structure and properties from solid-state inorganic and synthetic organic metals and semiconductors, supramolecular conductive proteins and peptides require careful theoretical treatment and experimental characterization methods to understand their electronic structure. In this review, we discuss theory and experimental evidence from recent literature describing the…

The ReaxFF protein reactive force field (protein-2013) has been successfully employed to simulate the biomolecules and membrane fuel cells, but it inaccurately describes the weak interaction of functionalized hydrocarbon/water molecules in condensed phase, especially for the density. In this article, the development of a ReaxFF force field (CHON-2017_weak) on the basis of protein-2013 is presented that improves the weak interaction description for atom pairs of carbon, hydrogen, oxygen, and nitrogen. To examine the quality of the force field, we performed a series of molecular dynamics simulations with model systems. These simulations, describing density trends for pure and mixture compound systems, demonstrate that CHON-2017_weak force field predictions are in good agreement with experimental data. Furthermore, ReaxFF can also describe the phase separation in hexane-water mixture and dissolution of ethanol or tetramethylammonium (TMA) in liquid water. To validate it in the application of membrane fuel cells, we studied structural property and degradation mechanism of TMA in…

The deep eutectic solvent glyceline formed by choline chloride and glycerol in 1:2 molar ratio is much less viscous compared to glycerol, which facilitates its use in many applications where high viscosity is undesirable. Despite the large difference in viscosity, we have found that the structural network of glyceline is completely defined by its glycerol constituent, which exhibits complex microscopic dynamic behavior, as expected from a highly correlated hydrogen-bonding network. Choline ions occupy interstitial voids in the glycerol network and show little structural or dynamic correlations with glycerol molecules. Despite the known higher long-range diffusivity of the smaller glycerol species in glyceline, in applications where localized dynamics is essential (e.g., in microporous media), the local transport and dynamic properties must be dominated by the relatively loosely bound choline ions.

The phase-change material, Ge 2 Sb 2 Te 5, is the canonical material ingredient for next-generation storage-class memory devices used in novel computing architectures, but fundamental questions remain regarding its atomic structure and physicochemical properties. Here, we introduce a machine-learning (ML)-based interatomic potential that enables large-scale atomistic simulations of liquid, amorphous, and crystalline Ge 2 Sb 2 Te 5 with an unprecedented combination of speed and density functional theory (DFT) level of accuracy. Two applications exemplify the usefulness of such an ML-driven approach: we generate a 7200-atom structural model, hitherto inaccessible with DFT simulations, that affords new insight into the medium-range structural order and we create an ensemble of uncorrelated, smaller structures, for studies of their chemical bonding with statistical significance. Our work opens the way for new atomistic insights into the fascinating and chemically complex class of phase-change materials that are used in real nonvolatile memory devices.

Motivated by the deficiencies of the previous MARTINI models of poly(ethylene oxide) (PEO), we present a new model featuring a high degree of transferability. The model is parametrized on (a) a set of 8 free energies of transfer of dimethoxyethane (PEO dimer) from water to solvents of varying polarity; (b) the radius of gyration in water at high dilution; and (c) matching angle and dihedral distributions from atomistic simulations. We demonstrate that our model behaves well in five different areas of application: (1) it produces accurate densities and phase behavior or small PEO oligomers and water mixtures; (2) it yields chain dimensions in good agreement with the experiment in three different solvents (water, diglyme, and benzene) over a broad range of molecular weights (∼1.2 kg/mol to 21 kg/mol); (3) it reproduces qualitatively the structural features of lipid bilayers containing PEGylated lipids in the brush and mushroom regime; (4) it is able to reproduce the phase behavior of several PEO-based nonionic surfactants in water; and (5) it can be combined with the existing MARTINI…

A simple and very sensitive electrochemical sensor for the detection of uric acid (UA) has been developed based on polyaniline (PANI) merged into a silver-doped iron oxide (Ag–Fe 2 O 3 ) nanocomposite-modified glassy carbon electrode. The synthesized ternary composite material (Ag–Fe 2 O 3 @PANI) was characterized by UV–visible spectroscopy, Fourier transform infrared spectroscopy, energy-dispersive X-ray, High-resolution transmission electron microscopy, X-ray diffraction, and thermo gravimetric analysis analyses. The nanocomposite-modified electrode shows an exceptional electrocatalytic activity and reversibility to the oxidation of UA in a 0.1 M phosphate buffer solution (pH 7.0) compared to those in PANI and Ag–Fe 2 O 3 . The detection limit of UA is found to be 102 pM with a linear dynamic range of 0.001–0.900 μM. The fabricated UA sensor also exhibits good selectivity, reproducibility, and long-time stability. The limit of detection and linear range attained for the synthesized composite are much greater compared to those of any other composite materials reported in the…

Oxidative stress (OS) is a health-threatening process that is involved, at least partially, in the development of several diseases. Although antioxidants can be used as a chemical defense against OS, they might also exhibit pro-oxidant effects, depending on environmental conditions. In this work, such a dual behavior was investigated for phenolic compounds (PhCs) within the framework of the density functional theory and based on kinetic data. Multiple reaction mechanisms were considered in both cases. The presence of redox metals, the pH, and the possibility that PhCs might be transformed into benzoquinones were identified as key aspects in the antioxidant versus pro-oxidant effects of these compounds. The main virtues of PhCs as antioxidants are their radical trapping activity, their regeneration under physiological conditions, and their behavior as OH-inactivating ligands. The main risks of PhCs as pro-oxidants are predicted to be the role of phenolate ions in the reduction of metal ions, which can promote Fenton-like reactions, and the formation of benzoquinones that might cause…

Far from the static, idealized conformations deposited into structural databases, proteins are highly dynamic molecules that undergo conformational changes on temporal and spatial scales that may span several orders of magnitude. These conformational changes, often intimately connected to the functional roles that proteins play, may be obscured by traditional biophysical techniques. Over the past 40 years, molecular dynamics (MD) simulations have complemented these techniques by providing the "hidden" atomistic details that underlie protein dynamics. However, there are limitations of the degree to which molecular simulations accurately and quantitatively describe protein motions. Here we show that although four molecular dynamics simulation packages (AMBER, GROMACS, NAMD, and ilmm) reproduced a variety of experimental observables for two different proteins (engrailed homeodomain and RNase H) equally well overall at room temperature, there were subtle differences in the underlying conformational distributions and the extent of conformational sampling obtained. This leads to ambiguity…

Several cyclic peptides have been reported to have unexpectedly high membrane permeability. Of these, cyclosporin A is perhaps the most well-known example, particularly in light of its relatively high molecular weight. Observations that cyclosporin A changes conformation depending on its solvent environment led to the hypothesis that conformational dynamics is a prerequisite for its permeability; however, this hypothesis has been difficult to validate experimentally. Here, we use molecular dynamics simulations to explicitly determine the conformational behavior of cyclosporin A and other related cyclic peptides as they spontaneously transition between different environments, including through a lipid bilayer. These simulations are referenced against simulations in explicit water, chloroform, and cyclohexane and further validated against NMR experiments, measuring conformational exchange, nuclear spin relaxation, and three-dimensional structures in membrane-mimicking environments, such as in dodecylphosphocholine micelles, to build a comprehensive understanding of the role of…

Abstract Spiropyrans undergo Cspiro–O bond breaking to their ring-open protonated E-merocyanine form upon protonation and irradiation via an intermediate protonated Z-merocyanine isomer. We show that the extent of acid-induced ring opening is controlled by matching both the concentration and strength of the acid used and with strong acids full ring opening to the Z-merocyanine isomer occurs spontaneously allowing its characterization by 1H NMR spectroscopy as well as UV/vis spectroscopy, and reversible switching between Z/E-isomerization by irradiation with UV and visible light. Under sufficiently acidic conditions, both E- and Z-isomers are thermally stable. Judicious choice of acid such that its pKa lies between that of the E- and Z-merocyanine forms enables thermally stable switching between spiropyran and E-merocyanine forms and hence pH gating between thermally irreversible and reversible photochromic switching.

Abstract Recrystallization of amorphous drugs is currently limiting the simple approach to improve solubility and bioavailability of poorly water-soluble drugs by amorphization of a crystalline form of the drug. In view of this, molecular mobility, α-relaxation and β-relaxation processes with the associated transition temperatures Tgα and Tgβ, was investigated using dynamic mechanical analysis (DMA). The correlation between the transition temperatures and the onset of recrystallization for nine amorphous drugs, stored under dry conditions at a temperature of 296 K, was determined. From the results obtained, Tgα does not correlate with the onset of recrystallization under the experimental storage conditions. However, a clear correlation between Tgβ and the onset of recrystallization was observed. It is shown that at storage temperature below Tgβ, amorphous nifedipine retains its amorphous form. On the basis of the correlation, an empirical correlation is proposed for predicting the onset of recrystallization for drugs stored at 0% RH and 296 K.

Fengycin is a cyclic lipopeptide used as an agricultural fungicide. It is synthesized by Bacillus subtilis as an immune response against fungal infection and functions by damaging the target's cell membrane. Previous molecular dynamics simulations and experiments have led to the hypothesis that the aggregation of fengycins on the membrane surface plays a key role in cell disruption. Here, we used microsecond-scale all-atom molecular dynamics simulations to understand the specificity, selectivity, and structure of fengycin oligomers. Our simulations suggest that fengycin is more likely to form stable oligomers in model fungal membranes (phosphatidylcholine) compared to the model bacterial membranes (phosphatidylethanolamine:phosphatidylglycerol). Furthermore, we characterize the differences in the structure and kinetics of the membrane-bound aggregates and discuss their functional implications.

One of the key limitations of Molecular Dynamics (MD) simulations is the computational intractability of sampling protein conformational landscapes associated with either large system size or long time scales. To overcome this bottleneck, we present the REinforcement learning based Adaptive samPling (REAP) algorithm that aims to efficiently sample conformational space by learning the relative importance of each order parameter as it samples the landscape. To achieve this, the algorithm uses concepts from the field of reinforcement learning, a subset of machine learning, which rewards sampling along important degrees of freedom and disregards others that do not facilitate exploration or exploitation. We demonstrate the effectiveness of REAP by comparing the sampling to long continuous MD simulations and least-counts adaptive sampling on two model landscapes (L-shaped and circular) and realistic systems such as alanine dipeptide and Src kinase. In all four systems, the REAP algorithm consistently demonstrates its ability to explore conformational space faster than the other two…

Perfluorosulfonic acid (PFSA) dispersions are used as components in a variety of electrochemical technologies, particularly in fuel-cell catalyst-layer inks. In this study, we characterize dispersions of a common PFSA, Nafion, as well as inks of Nafion and carbon. It is shown that solvent choice affects a dispersion's measured pH, which is found to scale linearly with Nafion loading. Dispersions in water-rich solvents are more acidic than those in propanol-rich solvents: a 90% water versus 30% water dispersion can have up to a 55% measured proton deviation. Furthermore, because electrostatic interactions are a function of pH, these differences affect how particles aggregate in solution. Despite having different water contents, all inks studied demonstrate the same particle size and surface charge trends as a function of pH, thus providing insights into the relative influence of solvent and pH effects on these properties.

It is widely appreciated that the addition of salts to water leads to significant changes in the thermodynamic and dynamic properties of these aqueous solutions that have great significance in biology and manufacturing applications. However, no theoretical framework currently exists that describes these property changes in an internally consistent fashion. In previous work, we developed a coarse-grained model of electrolyte solutions capable of reproducing basic trends on how salts influence the viscosity and water diffusion coefficient. The present work explores the predictions of this model for basic thermodynamic properties of electrolyte solutions, namely, the density, isothermal compressibility, and surface tension. On the basis of our model, we find that ion-specific effects on thermodynamics properties, and by extension the dynamics of electrolyte solutions, derive primarily from ion solvation.

Abstract Biomolecular simulations are typically performed in an aqueous environment where the number of ions remains fixed for the duration of the simulation, generally with either a minimally neutralizing ion environment or a number of salt pairs intended to match the macroscopic salt concentration. In contrast, real biomolecules experience local ion environments where the salt concentration is dynamic and may differ from bulk. The degree of salt concentration variability and average deviation from the macroscopic concentration remains, as yet, unknown. Here, we describe the theory and implementation of a Monte Carlo osmostat that can be added to explicit solvent molecular dynamics or Monte Carlo simulations to sample from a semigrand canonical ensemble in which the number of salt pairs fluctuates dynamically during the simulation. The osmostat reproduce the correct equilibrium statistics for a simulation volume that can exchange ions with a large reservoir at a defined macroscopic salt concentration. To achieve useful Monte Carlo acceptance rates, the method makes use of…

The associative memory, water-mediated, structure and energy model (AWSEM) has been successfully used to study protein folding, binding, and aggregation problems. In this work, we introduce AWSEM-IDP, a new AWSEM branch for simulating intrinsically disordered proteins (IDPs), where the weights of the potentials determining secondary structure formation have been finely tuned, and a novel potential is introduced that helps to precisely control both the average extent of protein chain collapse and the chain's fluctuations in size. AWSEM-IDP can efficiently sample large conformational spaces, while retaining sufficient molecular accuracy to realistically model proteins. We applied this new model to two IDPs, demonstrating that AWSEM-IDP can reasonably well reproduce higher-resolution reference data, thus providing the foundation for a transferable IDP force field. Finally, we used thermodynamic perturbation theory to show that, in general, the conformational ensembles of IDPs are highly sensitive to fine-tuning of force field parameters.

The interplay of degree of methylesterification (DM), pH, temperature, and concentration on the macromolecular interactions of pectin in solution has been explored. Small-angle X-ray scattering complemented by atomic force microscopy and molecular dynamics was employed to probe chain dimensions and solution structure. Two length scales have been observed with the first level of structure characterising chain clusters with sizes ranging between 100-200 nm. The second level of structure arises from single biopolymer chains with a radius of gyration between ∼6 and 42 nm. The development of a range of macromolecular dimensions in vitro and in silico shows that the chain flexibility increases with DM and at acidic pH, whereas hydrogen bonding is the responsible thermodynamic driving force for cluster formation. High methyl pectins create structures of lower fractal dimension with less efficient packing. This work unveils pectin conformations covering most of its industrially and biologically relevant environments, enabling rational design of advanced biomaterials based on pectin.

Binding affinities and stoichiometries of Na + and Ca 2+ ions to phospholipid bilayers are of paramount significance in the properties and functionality of cellular membranes. Current estimates of binding affinities and stoichiometries of cations are, however, inconsistent due to limitations in the available experimental and computational methods. In this work, we improve the description of the binding details of Na + and Ca 2+ ions to a 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer by implicitly including electronic polarization as a mean field correction, known as the electronic continuum correction (ECC). This is applied by scaling the partial charges of a selected state-of-the-art POPC lipid model for molecular dynamics simulations. Our improved ECC-POPC model reproduces not only the experimentally measured structural parameters for the ion-free membrane, but also the response of lipid headgroup to a strongly bound cationic amphiphile, as well as the binding affinities of Na + and Ca 2+ ions. With our new model, we observe on the one side negligible binding of Na +…

Drying and crystallization of solution droplets is a problem of broad relevance, determining the microstructures of particles formed in spray-drying, the phase of particles delivered by, for example, aerosol formulations for inhalation therapies, and the impact of aerosols on radiative forcing and climate. The ephemeral nature of free droplets, particularly when considering the drying kinetics of droplets with highly volatile constituents, has often precluded the accurate measurement of transient properties such as droplet size and composition, preventing the robust assessment of predictive models of droplet-drying rates, nucleation, and crystallization. Here, we report novel measurements of the drying kinetics of individual aqueous sodium chloride solution droplets using an electrodynamic balance to isolate and trap single aerosol droplets (radius ≈ 25 μm). The initial solution droplet size and composition are shown to be highly reproducible in terms of drying rate and crystallization time when examined over hundreds of identical evaporating droplets. We introduce a numerical model…

In view of recent intense experimental and theoretical interests in the biophysics of liquid–liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs), heteropolymer models with chain molecules configured as self-avoiding walks on the simple cubic lattice are constructed to study how phase behaviors depend on the sequence of monomers along the chains. To address pertinent general principles, we focus primarily on two fully charged 50-monomer sequences with significantly different charge patterns. Each monomer in our models occupies a single lattice site, and all monomers interact via a screened pairwise Coulomb potential. Phase diagrams are obtained by extensive Monte Carlo sampling performed at multiple temperatures on ensembles of 300 chains in boxes of sizes ranging from 52 × 52 × 52 to 246 × 246 × 246 to simulate a large number of different systems with the overall polymer volume fraction ϕ in each system varying from 0.001 to 0.1. Phase separation in the model systems is characterized by the emergence of a large cluster connected by intermonomer…

Macroporous hydrogel monoliths having tailor-made features, conductivity, superstretchability, excellent biocompatibility, and biodegradability, have become the most nurtured field of interest in soft biomaterials. Green method assisted reduced graphene oxide has been inserted by in situ free radical gelation into semi-IPN hydrogel matrix to fabricate conducting hydrogel. Mechanical toughness has been implemented for the graphene-polymer physisorption interactions with graphene basal planes. Moreover, the as-prepared 3D scaffold type monolith hydrogel has been rheologically superior regarding their high elastic modulus and delayed gel rupturing. κ-Carragenaan, one of the components of the hydrogel, has biodegradable nature. The most significant outcome is their low electrical percolation threshold and reversibly ductile nature. Reversible ductility provides them with rubber-like consistency in flow conditions. Surprising, the hydrogels showed dual stimuli-responsiveness, that is, environmental pH and external electrical stimulation. Electro-stimulation has been adopted here for the…

This Review Article highlights the utility of the fluorescence resonance energy transfer (FRET) to probe the dynamics and related issues in amphiphilic polymeric aggregates and supramolecular polymers. Amphiphilic polymers are more attractive compared to their small molecule analogues because they exhibit significantly lower critical aggregation concentration, relatively larger particle size (suitable for the enhanced permeation and retention effect), and a much slower dynamics of exchange between the unimer and the aggregate. Representative examples of exchange dynamics in amphiphilic polymer aggregates and their noncovalent encapsulation stability as a function of the structure of the macromolecule, cross-linking, environmental parameters, and biological conditions, as probed by FRET studies, have been included in this article. Further, related observations on the utility of FRET in studying the exchange dynamics in supramolecular polymers, particularly in aqueous medium, have been discussed at length, revealing a strong impact of chirality, side chain polarity, and other…

The temperature dependence of the vibrational sum-frequency generation (vSFG) spectra of the air/water interface is investigated using many-body molecular dynamics (MB-MD) simulations performed with the MB-pol potential energy function. The vSFG spectra calculated for different polarization combinations are then analyzed in terms of molecular autocorrelation and cross-correlation contributions. To provide molecular-level insights into interfacial hydrogen-bonding topologies, which give rise to specific spectroscopic features, the vSFG spectra are further investigated by separating contributions associated with water molecules donating zero, one, or two hydrogen bonds to neighboring water molecules. This analysis suggests that the low frequency shoulder of the free OH peak which appears at ∼3600 cm –1 is primarily due to intermolecular couplings between both singly and doubly hydrogen-bonded molecules.

Quantifying ion association and collective dynamical processes in organic electrolytes is essential for fundamental property interpretation and optimization for electrochemical applications. The extent of ion correlation depends on both the ion concentration and dielectric strength of the solvent; ions may be largely uncorrelated in sufficiently high-dielectric solvents at low concentration, but properties of concentrated electrolytes are dictated by correlated and collective ion processes. In this work, we utilize molecular dynamics simulations to characterize ion association and collective ion dynamics in organic electrolytes composed of binary mixtures of 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM + ][BF 4 – ] and 1,2-dichloroethane, acetone, acetonitrile, and water solvents. We illustrate different physical regimes of characteristically distinct ion correlations for the systematic range of electrolyte concentrations and solvent dielectric strengths. Dilute electrolytes composed of low-dielectric solvents exhibit significant counterion correlation in the form of ion…

A reactive molecular dynamics simulation has been performed for the characterization of the relationship between proton transport and water clustering in polymer electrolyte membranes. We have demonstrated that the anharmonic two-state empirical valence bond model is capable of describing efficiently excess proton transport through the Grotthuss hopping mechanism within the simplicity of the theoretical framework. To explore the long-time diffusion behavior in perfluorosulfonic acid membranes with statistical certainty, simulations that are longer than 10 ns are needed. The contribution of the Grotthuss mechanism to the proton transport yields a larger fraction compared to the vehicular mechanism, when the estimated percolation threshold of λ = 5.6 is surpassed. The cluster analyses elicit a consistent outlook in regard to the relationship between the connectivity and the confinement of water clusters and proton transport. The cluster growth behavior findings reveal that, below the percolation threshold, the water domains grow along the channel length to form the connected,…

An increasing demand for freshwater inspires further understanding of the mechanism of water diffusion in reverse-osmosis membranes for the development of high-performance membranes for desalination. Water diffusion has a close relationship with the structural and dynamical characteristics of hydrogen bonds, which is not well-understood for the confining environment inside the polyamide membrane at the molecular level. In this work, an atomistic model of a highly cross-linked polyamide membrane was built with an equilibrated mixture of m-phenylenediamine and trimesoyl chloride monomers. The structure and dynamics of water in the regions from the bulk phase to the membrane interior were investigated by molecular dynamics simulations. Explicit hydrogen bond criteria were determined for hydrogen-bonding analysis. The local distribution and orientation of water reveal that the hydrogen-bonding affinity of the hydrophilic functional groups of polymers inhibits water diffusion inside the membrane. The affinity helps to produce percolated water channels across the membrane. The…

Superconcentrated electrolyte solutions are receiving increasing attention as a novel class of liquid electrolyte for secondary batteries because of their unusual and favorable characteristics, which arise from a unique solution structure with a very small number of free solvent molecules. The present theoretical study investigates the concentration dependence of the structural and dynamical properties of these electrolyte solutions for Na-ion batteries using large-scale quantum molecular dynamics simulations. Microscopic analysis of the dynamical properties of Na + ions reveals that ligand (solvent/anion) exchange reactions, an alternative diffusion pathway for Na + ions, are responsible for carrier ion diffusion in the superconcentrated conditions.

In this work, we report the electric-field effects on ionic hydration of Cl –, Na +, and Pb 2+ using molecular dynamics simulations. It is found that the effect of weak fields on ionic hydration can be neglected. Strong fields greatly disturb the water orientation in the hydration shells of ions, though ion coordination number remains almost unchanged. Under strong fields, the first hydration shell of ions is significantly weakened and the ion–water interaction energy is dramatically reduced; surprisingly, the second hydration shells of Cl – and Na + are slightly structured because of the optimal water orientation; moreover, ionic hydration structures become asymmetrical along the field direction because of the uniformly aligned water dipoles. Compared with Na + and Pb 2+, the hydration of Cl – is less disturbed by external fields, probably ascribed to the different water reorientation around anions and cations as well as the different structure-maker/breaker nature of the ions. Additionally, strong fields significantly enhance ion mobility and remarkably shorten the water residence…

The structural and dynamical changes in the solvation shell surrounding Li + in a multianion environment are studied by Raman spectroscopy and molecular dynamics (MD) simulations. The ternary electrolyte is composed of a mixture of two ionic liquids (ILs), n -methyl- n -propylpyrrolidinium bis(trifluoromethanesulfonyl)imide ([PYR13][TFSI]) and 1-ethyl-3-methylimidazolium dicyanamide ([EMIM][DCA]), and a lithium bis(trifluoromethanesulfonyl)imide ([Li][TFSI]) salt (0–1 M). A 1:9 volumetric mixture of [PYR13][TFSI]/[EMIM][DCA] formed an eutectic that exhibited a lower melting point than that of either parent IL. The local structure of Li + in this eutectic is found to be heterogenous and preferentially solvated by [DCA], which is the smaller and more abundant anion. Whereas [TFSI] is able to bridge multiple Li + at high salt concentrations and form both monodentate and bidentate conformations through its oxygen atoms, [DCA] is capable of forming only monodentate coordination with Li + through either of its end nitrogen atoms. The Raman and MD analyses suggest a wide distribution of…

Abstract The structure factor and oxygen–oxygen pair-distribution functions of amorphous ices at liquid nitrogen temperature (T = 77 K) have been derived from wide-angle X-ray scattering (WAXS) up to interatomic distances of r = 23 Å, where local structure differences between the amorphous ices can be seen for the entire range. The distances to the first coordination shell for low-, high-, and very-high-density amorphous ice (LDA, HDA, VHDA) were determined to be 2.75, 2.78, and 2.80 Å, respectively, with high accuracy due to measurements up to a large momentum transfer of 23 Å–1. Similarities in pair-distribution functions between LDA and supercooled water at 254.1 K, HDA and liquid water at 365.9 K, and VHDA and high-pressure liquid water were found up to around 8 Å, but beyond that at longer distances, the similarities were lost. In addition, the structure of the high-density amorphous ices was compared to high-pressure crystalline ices IV, IX , and XII, and conclusions were drawn about the local ordering.

In experimental studies, it has been observed that the presence of sodium dodecyl sulfate (SDS) significantly increases the kinetics of hydrate formation and the final water-to-hydrate conversion ratio. In this study, we intend to understand the molecular mechanism behind the effect of SDS on the formation of methane hydrate through molecular dynamics simulation. Hydrate formation conditions similar to that of laboratory experiments were chosen to study hydrate growth kinetics in 1 wt % SDS solution. We also investigate the effect of interactions with isolated SDS molecules on methane hydrate growth. It was observed that the hydrophobic tail part of the SDS molecule favorably interacts with the growing hydrate surface and may occupy the partial hydrate cages while the head groups remain exposed to water.

Yb 3+ /Al 3+ /P 5+ -co-doped silica glasses with different P/Al ratios were prepared using the sol–gel method combined with high-temperature sintering. The evolution of composition-dependent color centers caused by X-ray irradiation in these glasses was correlated with their structural changes, which are controlled by the P/Al ratio. Nuclear magnetic resonance (NMR) and Raman spectra have been used to characterize the glass network structure, and advanced pulse electron paramagnetic resonance (EPR) has been employed to study the local coordination atomic structures of Yb 3+ ions in pristine glasses as a function of the P/Al ratio. Si- (Si-E′), Al- (Al-E′, Al-ODC, AlOHC), P- (P 1, P 2, POHC), and Yb-related (Yb 2+ ) color centers in irradiated glasses have been observed and explained by optical absorption and continuous wave-EPR spectroscopies. The formation mechanisms of these centers, the structural models of glasses, and the relationship between them were proposed. Direct evidence confirms that the formation of Yb 2+ ions induced by radiation is highly dependent on the…

Two-dimensional spectroscopy is a powerful tool for extracting structural and dynamic information from a wide range of chemical systems. We provide a brief overview of the ways in which two-dimensional visible and infrared spectroscopies are being applied to elucidate fundamental details of important processes in biological and materials science. The topics covered include amyloid proteins, photosynthetic complexes, ion channels, photovoltaics, batteries, as well as a variety of promising new methods in two-dimensional spectroscopy.

Rapid and accurate binding affinity prediction of protein–carbohydrate complexes is a major challenge in glycomimetics design. Among the existing computational techniques, end-point methods have received considerable interest because of their low computational cost. However, significant obstacles remain when such methods are applied to protein–glycan complexes. This article reports the performance of end-point free-energy calculation methods: molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA), MM/generalized Born surface area (MM/GBSA), and quantum mechanics–MM/GBSA (QM–MM/GBSA) on monosaccharides bound to RSL lectin from Ralstonia solanacearum . A careful investigation of the molecular dynamics simulation length, van der Waals radii sets, GB models, QM Hamiltonians, and entropic compensation has been made, and the results are compared with the experimental binding free energies from isothermal titration calorimetry/surface plasmon resonance measurements. The binding free energies using implicit solvent methods are found to be sensitive to the simulation length, radii set,…

The present study aims at the extraction of a polyaromatic hydrocarbon from fuel oils using a novel low-cost deep eutectic solvent (DES). The DES is prepared by mixing the hydrogen bond acceptor (HBA; methyltriphenylphosphonium bromide, MTPB) and hydrogen bond donor (HBD; ethylene glycol) at a molar ratio of 1:4. The liquid-liquid equilibrium is then measured at ambient condition. The classical molecular dynamic (MD) simulation technique is then employed to investigate and compare the experimental phase behavior of a DES-quinoline-heptane ternary system. For performing the MD simulations, two experimental feed points are considered which gave high selectivity and distribution coefficient values. The interaction energies of different species and the structural properties such as radial distribution functions, average number of hydrogen bonds, and spatial distribution functions (SDFs) are then computed. It is found that the cation within the HBA, namely, MTP, possesses favorable interactions with quinoline when compared to HBD or anion (Br). MTP here acts as a HBA and contributes to…

The computation of Kirkwood-Buff integrals (KBIs) using molecular simulations of closed systems is challenging due to finite system-size effects. One of the problems involves the incorrect asymptotic behavior of the radial distribution function. Corrections to rectify such effects have been proposed in the literature. This study reports a systematic comparison of the proposed corrections (as given by Ganguly et al. J. Chem. Theory Comput. 2013, 9, 1347-1355 and Krüger et al. J. Phys. Chem. Lett. 2013, 4, 4-7) to assess the asymptotic behavior of the RDFs, the KBIs, as well as the estimation of thermodynamic quantities for ideal urea-water and nonideal modified-urea-water mixtures using molecular dynamics simulations. The results show that applying the KBI correction suggested by Krüger et al. on the RDF corrected with the Ganguly et al. correction (denoted as B-KBI) yields improved KBI convergence for the ideal and nonideal aqueous mixtures. Different averaging regions in the running KBIs (correlated or long-range) are assessed, and averaging over the correlated region for large…

Aluminosilicate glasses are considered to follow the Al-avoidance principle, which states that Al–O–Al linkages are energetically less favorable, such that, if there is a possibility for Si–O–Al linkages to occur in a glass composition, Al–O–Al linkages are not formed. The current paper shows that breaching of the Al-avoidance principle is essential for understanding the distribution of network-forming AlO 4 and SiO 4 structural units in alkaline-earth aluminosilicate glasses. The present study proposes a new modified random network (NMRN) model, which accepts Al–O–Al linkages for aluminosilicate glasses. The NMRN model consists of two regions, a network structure region (NS-Region) composed of well-separated homonuclear and heteronuclear framework species and a channel region (C-Region) of nonbridging oxygens (NBOs) and nonframework cations. The NMRN model accounts for the structural changes and devitrification behavior of aluminosilicate glasses. A parent Ca- and Al-rich melilite-based CaO–MgO–Al 2 O 3 –SiO 2 (CMAS) glass composition was modified by substituting MgO for CaO and…

Molecular simulations of ionic liquids can provide deeper insight into the relationship between intermolecular interactions and macroscopic measurements for the solvents. However, many existing force fields have multiple shortcomings, including poor solvent dynamics, the underestimation of hydrogen-bonding strength, and errors in solvent interactions/organization. A new force field, called optimized potentials for liquid simulation-ionic-liquid virtual site (OPLS-VSIL), has been developed for imidazolium-based ionic liquids featuring a novel topology incorporating a virtual site bisecting the nitrogen atoms that offloads negative charge to inside the plane of the ring. Guided by free energy of hydration calculations, an empirically derived set of partial charges and nonbonded Lennard-Jones terms for both 1-alkyl-3-methylimidazolium and 11 different anions provided accurate bulk-phase ionic-liquid properties and produced radial distribution functions nearly indistinguishable from ab initio molecular dynamics simulations. For example, overall mean absolute errors (MAEs) of 3.1-3.4%…

We present experimental results on the phase behavior of block copolymer/salt mixtures over a wide range of copolymer compositions, molecular weights, and salt concentrations. The experimental system comprises polystyrene- block -poly(ethylene oxide) and lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) salt. It is well established that LiTFSI interacts favorably with poly(ethylene oxide) relative to polystyrene. The relationship between chain length and copolymer composition at fixed temperature is U-shaped, as seen in experiments on conventional block copolymers and as anticipated from the standard self-consistent field theory (SCFT) of block copolymer melts. The phase behavior can be explained in terms of an effective Flory–Huggins interaction parameter between the polystyrene monomers and poly(ethylene oxide) monomers complexed with the salt, χ eff, which increases linearly with salt concentration. The phase behavior of salt-containing block copolymers, plotted on a segregation strength versus copolymer composition plot, is similar to that of conventional (uncharged) block…

Nanoparticles made of amphiphilic block copolymers comprising biodegradable core-forming blocks are very attractive for the preparation of drug-delivery systems with sustained release. Their therapeutic applications are, however, hindered by low values of the drug-loading content (DLC). The compatibility between the drug and the core-forming block of the copolymer is considered the most important factor affecting the DLC value. However, the molecular picture of the hydrophobic drug-copolymer interaction is still not fully recognized. Herein, we examined this complex issue using a range of experimental techniques in combination with atomistic molecular dynamics simulations. We performed an analysis of the interaction between itraconazole, a model hydrophobic drug, and a poly(ethylene glycol)-poly(lactide- co-glycolide) (PEG-PLGA) copolymer, a biodegradable copolymer commonly used for the preparation of drug-delivery systems. Our results clearly show that the limited capacity of the PEG-PLGA nanoparticles for the accumulation of hydrophobic drugs is due to the fact that the drug…

Accurately predicting protein-ligand binding affinities and binding modes is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement, conformation, and orientations of a relatively rigid, fragment-like ligand in a receptor, and the populations of the multiple binding modes which may be relevant. This problem is important in its own right, but is even more timely given the recent success of alchemical free energy calculations. Alchemical calculations are increasingly used to predict binding free energies of ligands to receptors. However, the accuracy of these calculations is dependent on proper sampling of the relevant ligand binding modes. Unfortunately, ligand binding modes may often be uncertain, hard to predict, and/or slow to interconvert on simulation time scales, so proper sampling with current techniques can require prohibitively long simulations. We need new methods which…

The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus crucial to uncover the mystery of the hydration structure and dynamics as well as their coupling to collective motions of proteins in aqueous solutions. Here, we report dielectric properties of aqueous bovine serum albumin protein solutions as a model system using an extremely sensitive dielectric spectrometer with frequencies spanning from megahertz to terahertz. The dielectric relaxation spectra reveal several polarization mechanisms at the molecular level with different time constants and dielectric strengths, reflecting the complexity of protein-water interactions. Combining the effective-medium approximation and molecular dynamics simulations, we have determined collective vibrational modes at terahertz frequencies and the number of water molecules in the tightly bound and loosely bound hydration layers. High-precision measurements of the number of…

As frontal polymerization is being considered as a faster and more energy efficient manufacturing technique for polymer-matrix fiber-reinforced composites, we perform a finite-element-based numerical study of the initiation and propagation of a polymerization front in dicyclopentadiene (DCPD). The transient thermochemical simulations are complemented by an analytical study of the steady-state propagation of the polymerization front, allowing to draw a direct link between the cure kinetics model and the key characteristics of the front, i.e., front velocity and characteristic length scales. The second part of this study focuses on the prediction of the temperature spike associated with the merger of two polymerization fronts. The thermal peak, which might be detrimental to the properties of the polymerized material, is due to the inability of the heat associated with the highly exothermic reaction to be dissipated when the two fronts merge. The analysis investigates how the amplitude of the thermal spike is affected by the degree of cure at the time of the front merger.

A quantitative characterization of intermolecular and intramolecular couplings that modulate the OH-stretch vibrational band in liquid water has so far remained elusive. Here, we take up this challenge by combining the centroid molecular dynamics formalism, which accounts for nuclear quantum effects, with the MB-pol potential energy function, which accurately reproduces the properties of water across all phases, to model the infrared (IR) spectra of various isotopic water solutions with different levels of vibrational couplings, including those that cannot be probed experimentally. Analysis of the different IR OH-stretch line shapes provides direct evidence for the partially quantum-mechanical nature of hydrogen bonds in liquid water, which is emphasized by synergistic effects associated with intermolecular coupling and many-body electrostatic interactions. Furthermore, we quantitatively demonstrate that intramolecular coupling, which results in Fermi resonances due to the mixing between HOH-bend overtones and OH-stretch fundamentals, is responsible for the shoulder located at ∼3250…