Showing papers in "Journal of Physical Chemistry B in 2018"
TL;DR: 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 is developed.
Abstract: 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. Finally, we applied a generalized additive model (GAM) approach to the Rosetta energy function; the resulting nonlinear reweighting model improved the agreement with experimentally determined interface ΔΔ G values but also highlighted the necessity of future energy function improvements.
165 citations
TL;DR: It is demonstrated that Li+ hopping suppresses concentration polarization in Li batteries, leading to increased limiting current density and improved rate capability compared to the conventional concentration electrolyte.
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 molecu...
136 citations
TL;DR: The simulations indicate that water is more mobile than the other species and its addition also fosters faster motion of urea, and the microheterogeneous structure of these complex liquid mixtures is revealed.
Abstract: First-principles molecular dynamics simulations in the canonical ensemble at temperatures of 333 and 363 K and at the corresponding experimental densities are carried out to investigate the behavior of the 1:2 choline chloride/urea (reline) deep eutectic solvent and its equimolar mixture with water. Analysis of atom–atom radial and spatial distribution functions and of the H-bond network reveals the microheterogeneous structure of these complex liquid mixtures. In neat reline, the structure is governed by strong H-bonds of the trans- and cis-H atoms of urea to the chloride ion. In hydrous reline, water competes for the anions, and the H atoms of urea have similar propensities to bond to the chloride ions and the O atoms of urea and water. The vibrational spectra exhibit relatively broad peaks reflecting the heterogeneity of the environment. Although the 100 ps trajectories allow only for a qualitative assessment of transport properties, the simulations indicate that water is more mobile than the other spe...
128 citations
TL;DR: 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 shows that the decisive physicochemical parameters in autoxidation are the pK values of the semiquinone and the amino group in the oxidized quinone.
Abstract: 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 pK 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.
127 citations
TL;DR: 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 and gave near quantitative agreement at multiple temperatures for experimental densities, viscosities, heat capacities, and surface tensions.
Abstract: 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 accurate...
115 citations
TL;DR: Implementation of electronic band structure and electron transfer formulations in extended biomolecular systems will be covered in the context of recent materials discoveries and efforts at characterization of electronic transport mechanisms.
Abstract: 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 long-range conduction of electronic charge in protein and peptide materials Electron transfer across proteins has been studied extensively, but application of models for such short-range charge transport to longer distances relevant to bioelectronic materials are less well-understood Implementation of electronic band structure and electron transfer formulations in extended biomolecular systems will be covered in the context of recent materials discoveries and efforts at characterization of electronic transport mechanisms
110 citations
TL;DR: It is observed that LNPs form a layered structure, and it is detected that DSPC and DMPE-PEG 2000 lipids form a surface rich layer in the presence (or absence) of the cargoes and that the cholesterol and ionizable cationic lipid are embedded in the core.
Abstract: 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 1H-1H 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 a layered structure, and we detect that DSPC and DMPE-PEG 2000 lipids form a surface rich layer in the presence (or absence) of the cargoes and that the cholesterol and ionizable cationic lipid are embedded in the core. Furthermore, relayed DNP 31P solid-state NMR experiments allow the location of the cargo encapsulated in the LNPs to be determined. On the basis of the results, we propose a new structural model for the LNPs that features a homogeneous core with a tendency for layering of DSPC and DMPE-PEG at the surface.
107 citations
TL;DR: The results of kinetic tests and ambient-pressure X-ray photoelectron spectroscopy show the important role played by a ZnO-copper interface in the generation of CO and the synthesis of methanol from CO2 hydrogenation.
Abstract: The results of kinetic tests and ambient-pressure X-ray photoelectron spectroscopy (AP-XPS) show the important role played by a ZnO-copper interface in the generation of CO and the synthesis of methanol from CO2 hydrogenation. The deposition of nanoparticles of ZnO on Cu(100) and Cu(111), θoxi < 0.3 monolayer, produces highly active catalysts. The catalytic activity of these systems increases in the sequence: Cu(111) < Cu(100) < ZnO/Cu(111) < ZnO/Cu(100). The structure of the copper substrate influences the catalytic performance of a ZnO-copper interface. Furthermore, size and metal-oxide interactions affect the chemical and catalytic properties of the oxide making the supported nanoparticles different from bulk ZnO. The formation of a ZnO-copper interface favors the binding and conversion of CO2 into a formate intermediate that is stable on the catalyst surface up to temperatures above 500 K. Alloys of Zn with Cu(111) and Cu(100) were not stable at the elevated temperatures (500-600 K) used for the CO2 hydrogenation reaction. Reaction with CO2 oxidized the zinc, enhancing its stability over the copper substrates.
106 citations
TL;DR: A machine-learning (ML)-based interatomic potential is introduced that enables large-scale atomistic simulations of liquid, amorphous, and crystalline Ge2Sb2Te5 with an unprecedented combination of speed and density functional theory (DFT) level of accuracy.
Abstract: The phase-change material, Ge2Sb2Te5, 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 Ge2Sb2Te5 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...
100 citations
TL;DR: It is 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.
Abstract: 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.
100 citations
TL;DR: It is shown that one can map the molecular Hamiltonian to an Ising-type Hamiltonian which could easily be implemented on currently available quantum hardware and is an early step in developing generalized methods on such devices for chemical physics.
Abstract: Obtaining exact solutions to the Schrodinger equation for atoms, molecules, and extended systems continues to be a “Holy Grail” problem which the fields of theoretical chemistry and physics have been striving to solve since inception. Recent breakthroughs have been made in the development of hardware-efficient quantum optimizers and coherent Ising machines capable of simulating hundreds of interacting spins with an Ising-type Hamiltonian. One of the most vital questions pertaining to these new devices is, “Can these machines be used to perform electronic structure calculations?” Within this work, we review the general procedure used by these devices and prove that there is an exact mapping between the electronic structure Hamiltonian and the Ising Hamiltonian. Additionally, we provide simulation results of the transformed Ising Hamiltonian for H2 , He2 , HeH+, and LiH molecules, which match the exact numerical calculations. This demonstrates that one can map the molecular Hamiltonian to an Ising-type Hami...
TL;DR: It is shown that at storage temperature below Tgβ, amorphous nifedipine retains its amorphously form and an empirical correlation is proposed for predicting the onset of recrystallization for drugs stored at 0% RH and 296 K.
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 dr...
TL;DR: 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.
Abstract: 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 0001 to 01 Phase separation in the model systems is characterize
TL;DR: It is found that conformational flexibility is a key determinant of the membrane permeability of cyclosporin A and similar membrane-permeable cyclic peptides, as conformationally constrained variants have limited movement into, then through, and finally out of the membranes in silico.
Abstract: 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 dynamics. We find that conformational flexibility is a key determinant of the membrane permeability of cyclosporin A and similar membrane-permeable cyclic peptides, as conformationally constrained variants have limited movement into, then through, and finally out of the membrane in silico. We envisage that a better understanding of dynamics might thus provide new opportunities to modulate peptide function and enhance their delivery.
TL;DR: In this article, a reinforcement learning based adaptive samPling (REAP) algorithm is proposed to sample conformational space by learning the relative importance of each order parameter as it samples the landscape.
Abstract: 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 methods when comparing the expected values of the landscape discovered for a given amount of time. The key advantage of REAP is on-the-fly estimation of the importance of collective variables, which makes it particularly useful for systems with limited structural information.
TL;DR: The present work explores the predictions of this model for basic thermodynamic properties of electrolyte solutions, namely, the density, isothermal compressibility, and surface tension and finds that ion-specific effects on thermodynamics properties, and by extension the dynamics of electrolytes solutions, derive primarily from ion solvation.
Abstract: 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.
TL;DR: The 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 Ca2+ ions.
Abstract: Binding affinities and stoichiometries of Na+ and Ca2+ 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 Ca2+ 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 Ca2+ ions. With...
TL;DR: The new PEO model outperforms previous models and features a high degree of transferability and can be combined with the existing MARTINI PS to model PS-PEO block copolymers.
Abstract: 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 nonio...
TL;DR: This work introduces 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.
Abstract: 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-tun...
TL;DR: The proposed method has been successfully applied for the selective detection of UA in various real samples such as human serum and urine with good recoveries and can be widely employed for fabricating diverse sensors.
Abstract: 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–Fe2O3) nanocomposite-modified glassy carbon electrode. The synthesized ternary composite material (Ag–Fe2O3@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–Fe2O3. 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 compar...
TL;DR: This work shows that the surface properties of active OER catalysts, such as RuO2, can be tuned to achieve higher electrocatalytic stability in PEM electrolyzers, and elucidate the importance of submonolayer surface IrOx in minimizing Ru dissolution.
Abstract: The high precious metal loading and high overpotential of the oxygen evolution reaction (OER) prevents the widespread utilization of polymer electrolyte membrane (PEM) water electrolyzers. Herein we explore the OER activity and stability in acidic electrolyte of a combined IrOx/RuO2 system consisting of RuO2 thin films with submonolayer (1, 2, and 4 A) amounts of IrOx deposited on top. Operando extended X-ray absorption fine structure (EXAFS) on the Ir L-3 edge revealed a rutile type IrO2 structure with some Ir sites occupied by Ru, IrOx being at the surface of the RuO2 thin film. We monitor corrosion on IrOx/RuO2 thin films by combining electrochemical quartz crystal microbalance (EQCM) with inductively coupled mass spectrometry (ICP-MS). We elucidate the importance of submonolayer surface IrOx in minimizing Ru dissolution. Our work shows that we can tune the surface properties of active OER catalysts, such as RuO2, aiming to achieve higher electrocatalytic stability in PEM electrolyzers.
TL;DR: Electrochemical measurements and density functional theory calculations revealed that enhanced activity of Co-modified Ni Fe LDH could be attributed to the ability of Co to tune the electronic structure of the NiFe LDH so that optimal binding of OER reaction intermediates could be achieved.
Abstract: We present a combined experimental and theoretical study to demonstrate that the electrocatalytic activity of NiFe layered double hydroxides (NiFe LDHs) for the oxygen evolution reaction (OER) can be significantly enhanced by systematic cobalt incorporation using coprecipitation and/or intercalation. Electrochemical measurements show that cobalt modified NiFe LDH possesses an enhanced activity for the OER relative to pristine NiFe LDH. The Co-modified NiFe LDH exhibits overpotentials in the range of 290–322 mV (at 10 mA cm–2), depending on the degree of cobalt content. The best catalyst, cobalt intercalated NiFe LDH achieved a current density of 10 mA cm–2 at an overpotential of ∼265 mV (compared to 310 mV for NiFe LDH), with a near unity (99%) faradaic efficiency and long-term stability. Density functional theory calculations revealed that enhanced activity of Co-modified NiFe LDH could be attributed to the ability of Co to tune the electronic structure of the NiFe LDH so that optimal binding of OER reac...
TL;DR: This paper used classification via random forests to predict the stability of half-Heusler (HH) compounds, using only experimentally reported compounds as a training set Cross-validation yields an excellent agreement between the fraction of compounds classified as stable and the actual fraction of truly stable compounds in the ICSD.
Abstract: Machine learning (ML) is increasingly becoming a helpful tool in the search for novel functional compounds Here we use classification via random forests to predict the stability of half-Heusler (HH) compounds, using only experimentally reported compounds as a training set Cross-validation yields an excellent agreement between the fraction of compounds classified as stable and the actual fraction of truly stable compounds in the ICSD The ML model is then employed to screen 71 178 different 1:1:1 compositions, yielding 481 likely stable candidates The predicted stability of HH compounds from three previous high-throughput ab initio studies is critically analyzed from the perspective of the alternative ML approach The incomplete consistency among the three separate ab initio studies and between them and the ML predictions suggests that additional factors beyond those considered by ab initio phase stability calculations might be determinant to the stability of the compounds Such factors can include conf
TL;DR: This work combines neutron scattering experiments in a specific mixture of H2O and D2O with ab initio molecular dynamics simulations to probe the difference in the hydration structure and ion-pairing properties of chloride solutions of the two cations and shows that using this electronic continuum correction it can describe aqueous magnesium chloride solutions well.
Abstract: Magnesium and zinc dications possess the same charge and have an almost identical size, yet they behave very differently in aqueous solutions and play distinct biological roles. It is thus crucial to identify the origins of such different behaviors and to assess to what extent they can be captured by force-field molecular dynamics simulations. In this work, we combine neutron scattering experiments in a specific mixture of H2O and D2O (the so-called null water) with ab initio molecular dynamics simulations to probe the difference in the hydration structure and ion-pairing properties of chloride solutions of the two cations. The obtained data are used as a benchmark to develop a scaled-charge force field for Mg2+ that includes electronic polarization in a mean field way. We show that using this electronic continuum correction we can describe aqueous magnesium chloride solutions well. However, in aqueous zinc chloride specific interaction terms between the ions need to be introduced to capture ion pairing q...
TL;DR: Surprising, the hydrogels showed dual stimuli-responsiveness, that is, environmental pH and external electrical stimulation, in semi-IPN systems, which could be an ideal alternative for iontopheretic devices and pulsatile drug release through skin.
Abstract: 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 exte...
TL;DR: It is shown 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/visSpectroscopy, and reversible switching between Z/E-isomerization by irradiation with UV and visible light.
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.
TL;DR: 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.
Abstract: 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 ce...
TL;DR: This study reports comprehensively how the combination band acts as an intrinsic and collective probe in various chemically and biologically relevant solutions, including salts of varying character, denaturants, osmolytes, crowders, and surfactants that form reverse micells and micelles.
Abstract: Water is an extensively self-associated liquid due to its extensive hydrogen bond (H-bond) forming ability. The resulting H-bonded network fluid exhibits nearly continuous absorption of light from the terahertz to the near-IR region. The relatively weak bend+libration water combination band (centered at 2130 cm–1) has been largely overlooked as a reporter of liquid water’s structure and dynamics despite its location in a convenient region of the IR for spectroscopic study. The intermolecular nature of the combination band leads to a unique absorption signal that reports collectively on the rigidity of the H-bonding network in the presence of many different solutes. This study reports comprehensively how the combination band acts as an intrinsic and collective probe in various chemically and biologically relevant solutions, including salts of varying character, denaturants, osmolytes, crowders, and surfactants that form reverse micelles and micelles. While we remark on changes in the line width and intensi...
TL;DR: Observations indicate that the ultrathin layer containing cobalt oxyhydroxide is the active phase for oxygen evolution reaction (OER) on a Co electrode in an alkaline electrolyte, consistent with previous studies.
Abstract: Recent advances of ambient pressure X-ray photoelectron spectroscopy (AP-XPS) have enabled the chemical composition and the electrical potential profile at a liquid/electrode interface under electrochemical reaction conditions to be directly probed. In this work, we apply this operando technique to study the surface chemical composition evolution on a Co metal electrode in 0.1 M KOH aqueous solution under various electrical biases. It is found that an ∼12.2 nm-thick layer of Co(OH)2 forms at a potential of about -0.4 VAg/AgCl, and upon increasing the anodic potential to about +0.4 VAg/AgCl, this layer is partially oxidized into cobalt oxyhydroxide (CoOOH). A CoOOH/Co(OH)2 mixture layer is formed on the top of the electrode surface. Finally, the oxidized surface layer can be reduced to Co0 at a cathodic potential of -1.35 VAg/Cl. These observations indicate that the ultrathin layer containing cobalt oxyhydroxide is the active phase for oxygen evolution reaction (OER) on a Co electrode in an alkaline electrolyte, consistent with previous studies.
TL;DR: It is shown that solvent choice affects a dispersion's measured pH, which is found to scale linearly with Nafion loading, and 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.
Abstract: 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.