The small molecule activator S3969 stimulates the epithelial sodium channel by interacting with a specific binding pocket in the channel's ß-subunit.

The epithelial sodium channel (ENaC) is essential for mediating sodium absorption in several epithelia. Its impaired function leads to severe disorders, including pseudohypoaldosteronism type 1 and respiratory distress. Therefore, pharmacological ENaC activators have potential therapeutic implications. Previously, a small molecule ENaC activator (S3969) was developed. So far, little is known about molecular mechanisms involved in S3969-mediated ENaC stimulation. Here, we identified an S3969-binding site in human ENaC by combining structure-based simulations with molecular biological methods and electrophysiological measurements of ENaC heterologously expressed in Xenopus laevis oocytes. We confirmed a previous observation that the extracellular loop of ß-ENaC is essential for ENaC stimulation by S3969. Molecular dynamics simulations predicted critical residues in the thumb domain of ß-ENaC (Arg388, Phe391, and Tyr406) that coordinate S3969 within a binding site localized at the ß-γ-subunit interface. Importantly, mutating each of these residues reduced (R388H; R388A) or nearly abolished (F391G; Y406A) the S3969-mediated ENaC activation. Molecular dynamics simulations also suggested that S3969-mediated ENaC stimulation involved a movement of the α5 helix of the thumb domain of ß-ENaC away from the palm domain of γ-ENaC. Consistent with this, the introduction of two cysteine residues (ßR437C - γS298C) to form a disulfide bridge connecting these two domains prevented ENaC stimulation by S3969 unless the disulfide bond was reduced by DTT. Finally, we demonstrated that S3969 stimulated ENaC endogenously expressed in cultured human airway epithelial cells (H441). These new findings may lead to novel (patho-)physiological and therapeutic concepts for disorders associated with altered ENaC function.

Organic Nucleation: Water Rearrangement Reveals the Pathway of Ibuprofen.

The organic nucleation of the pharmaceutical ibuprofen is investigated, as triggered by the protonation of ibuprofen sodium salt at elevated pH. The growth and aggregation of nanoscale solution species by Analytical Ultracentrifugation and Molecular Dynamics (MD) simulations is tracked. Both approaches reveal solvated molecules, oligomers, and prenucleation clusters, their size as well as their hydration at different reaction stages. By combining surface-specific vibrational spectroscopy and MD simulations, water interacting with ibuprofen at the air-water interface during nucleation is probed. The results show the structure of water changes upon ibuprofen protonation in response to the charge neutralization. Remarkably, the water structure continues to evolve despite the saturation of protonated ibuprofen at the hydrophobic interface. This further water rearrangement is associated with the formation of larger aggregates of ibuprofen molecules at a late prenucleation stage. The nucleation of ibuprofen involves ibuprofen protonation and their hydrophobic assembly. The results highlight that these processes are accompanied by substantial water reorganization. The critical role of water is possibly relevant for organic nucleation in aqueous environments in general.

Assessing Solid Catalysts with Ionic Liquid Layers (SCILL) from Molecular Dynamics Simulations: On the role of local charge polarization.

Recent developments in molecular mechanics modelling of metal catalyst surfaces with interfaces to complex ad-layers or bulk liquids enable the study of 10 nm scale systems by molecular dynamics simulations of up to microseconds. Therein, electronic polarization as otherwise benchmarked by quantum calculations is mimicked via atom-centered partial charges that are adjusted dynamically to account for changes in local environment. Apart from thermal fluctuations, this encompasses molecule association and dissociation processes as well as externally applied voltage. Here, we elaborate the concept of employing the charge equilibration method to the molecular dynamics simulation of solid catalysts, namely metal surfaces and substrate-supported metal nanoparticles. This showcases the association of reactants and their interplay with local charge polarization upon co-adsorption of ionic liquids or application of external voltage - thus paving the way to understanding complex interfaces in (electro-)catalysis from molecular dynamics simulation.

Self-Assembled Supported Ionic Liquids.

Separation and reuse of the catalytically active metal complexes are persistent issues in homogeneous catalysis. Supported Ionic Liquid Phase (SILP) catalysts, where the catalytic center is dissolved in a thin film of a stable ionic liquid, deposited on a solid support, present a promising alternative. However, the dissolution of the metal center in the film leaves little control over its position and its activity. We present here four novel, task-specific ionic liquids [FPhn ImH R]I (n=1, 2; R=PEG2 , C12 H25 ), designed to self-assemble on a silica surface without any covalent bonding and offering a metal binding site in a controlled distance to the support. Advanced multinuclear solid-state NMR spectroscopic techniques under Magic Angle Spinning, complemented by molecular dynamics (MD) simulations, allow us to determine their molecular conformation when deposited inside SBA-15 as a model silica support. We provide here conceptual proof for a rational design of ionic liquids self-assembling into thin films, opening an avenue for a second, improved generation of SILP catalysts.

Efficient Assessment of 'Instantaneous pK' Values from Molecular Dynamics Simulations.

We present a molecular simulation approach to studying the role of local and momentary molecular environment for potential acid-base reactions. For this, we combine thermodynamic considerations on the pK of ionic species with rapid sampling of energy changes related to (de)protonation. Using dispersed carbonate ions in water as a reference, our approach aims at the fast assessment of the momentary protonation energy, and thus the 'instantaneous pK', of calcium-carbonate ion aggregates. The latter include transient complexes that are elusive to long sampling runs. This motivated the elaboration of approximate, yet particularly fast assessable sampling strategies. Along this line, we were able to characterize instantaneous pK values at a statistical accuracy of 0.4 pK units within sampling runs of only 10 ps duration, whereas statistical errors reduce to 0.1 pK units in 75 ps sampling runs, respectively. This readily enabled the required time resolution for the characterization of [Cax (CO3 )y ]2(x-y) aggregates with x=1,2 and y=1,2,3, respectively. In turn, the analysis of the pH-dependent nature of calcite-water interfaces and dynamically ordered liquid-like oxyanion polymers (dollop) domains is outlined at 10 ps resolution.

Evolution of Surface Tension and Hansen Parameters of a Homologous Series of Imidazolium-Based Ionic Liquids.

In this study, we systematically analyze the surface tension and Hansen solubility parameters (HSPs) of imidazolium-based ionic liquids (ILs) with different anions ([NTf2]-, [PF6]-, [I]-, and [Br]-). These anions are combined with the classical 1-alkyl-3-methyl-substituted imidazolium cations ([CnC1Im]+) and a group of oligoether-functionalized imidazolium cations ([(mPEGn)2Im]+) based on methylated polyethylene glycol (mPEGn). In detail, the influences of the length of the alkyl- and the mPEGn-chain, the anion size, and the water content are investigated experimentally. For [CnC1Im]+-based ILs, the surface tension decreases with increasing alkyl chain length in all cases, but the magnitude of this decrease depends on the size of the anion ([NTf2]- < [PF6]- < [Br]- ≤ [I]-). Molecular dynamics (MD) simulations on [CnC1Im]+-based ILs indicate that these differences are caused by the interplay of charged and uncharged domains, in particular in the different anions, which affects the ability of the alkyl chains of the cation to orient toward the liquid-gas interface. An increase in the mPEGn-chain length of the [(mPEGn)2Im][A] ILs does not significantly influence the surface tension. These changes upon variation of the cation/anion combination do not correlate with the evolution of the HSPs for the two sets of ILs. Finally, our data suggest that significant water contents up to water mole fractions of x(H2O) = 0.25 do not significantly affect the surface tension of the studied binary IL-water mixtures.

Bottom-to-top modeling of epoxy resins: From atomic models to mesoscale fracture mechanisms.

We outline a coarse-grained model of epoxy resins (bisphenol-F-diglycidyl-ether/3,5-diethyltoluene-2,4-diamine) to describe elastic and plastic deformation, cavitation, and fracture at the µm scale. For this, molecular scale simulation data collected from quantum and molecular mechanics studies are coarsened into an effective interaction potential featuring a single type of beads that mimic 100 nm scale building blocks of the material. Our model allows bridging the time-length scale problem toward experimental tensile testing, thus effectively reproducing the deformation and fracture characteristics observed for strain rates of 10-1 to 10-5 s-1. This paves the way to analyzing viscoelastic deformation, plastic behavior, and yielding characteristics by means of "post-atomistic" simulation models that retain the molecular mechanics of the underlying epoxy resin at length scales of 0.1-10 µm.

Structure Formation in an Ionic Liquid Wetting Layer: A Combined STM, IRAS, DFT and MD Study of [C2 C1 Im][OTf] on Au(111).

In a solid catalyst with ionic liquid layer (SCILL), ionic liquid (IL) coatings are used to improve the selectivity of noble metal catalysts. To understand the origins of this selectivity control, we performed model studies by surface science methods in ultrahigh vacuum (UHV). We investigated the growth and thermal stability of ultrathin IL films by infrared reflection absorption spectroscopy (IRAS). We combined these experiments with scanning tunneling microscopy (STM) to obtain information on the orientation of the ions, the interactions with the surface, the intermolecular interactions, and the structure formation. Additionally, we performed DFT calculations and molecular dynamics (MD) simulations to interpret the experimental data. We studied the IL 1-ethyl-3-methylimidazolium trifluoromethanesulfonate [C2 C1 Im][OTf] on Au(111) surfaces. We observe a weakly bound multilayer of [C2 C1 Im][OTf], which is stable up to 390 K, while the monolayer desorbs at ∼450 K. [C2 C1 Im][OTf] preferentially adsorbs at the step edges and elbows of the herringbone reconstruction of Au(111). The anion adsorbs via the SO3 group with the molecular axis perpendicular to the surface. At low coverage, the [C2 C1 Im][OTf] crystallizes in a glass-like 2D phase with short-range order. At higher coverage, we observe a phase transition to a 6-membered ring structure with long-range order.

On the Role of Amides and Imides for Understanding GaN Syntheses from Ammonia Solution: Molecular Mechanics Models of Ammonia, Amide and Imide Interactions with Gallium Nitride.

A key requisite to characterizing GaN precipitation from ammonia solution from molecular simulations is the availability of reliable molecular mechanics models for the interactions of gallium ions with NH3 , NH2- , and NH2- species, respectively. Here, we present a tailor-made force field which is fully compatible to an earlier developed GaN model, thus bridging the analyses of Ga3+ ions in ammonia solution with the aggregation of [Gax (NH)y (NH2 )z ]+3x-2y-z precursors and the modelling of GaN crystals. For this, quantum mechanical characterization of a series of Ga-coordination clusters is used for parameterization and benchmarking the generalized amber force field (GAFF2) and tailor-made refinements needed to achieve good agreement of both structural features and formation energy, respectively. The perspectives of our models for larger scale molecular dynamics simulations are demonstrated by the analyses of amide and imide defects arrangement during the growth of GaN crystal faces.

A group of cationic amphiphilic drugs activates MRGPRX2 and induces scratching behavior in mice.

BACKGROUND: Mas gene-related G protein-coupled receptors (MRGPRs) are a G protein-coupled receptor family responsive to various exogenous and endogenous agonists, playing a fundamental role in pain and itch sensation. The primate-specific family member MRGPRX2 and its murine orthologue MRGPRB2 are expressed by mast cells mediating IgE-independent signaling and pseudoallergic drug reactions. OBJECTIVES: Our aim was to increase knowledge about the function and regulation of MRGPRX2/MRGPRB2, which is of major importance in prevention of drug hypersensitivity reactions and drug-induced pruritus. METHODS: To identify novel MRGPR (ant)agonists, we screened a library of pharmacologically active compounds by utilizing a high-throughput calcium mobilization assay. The identified hit compounds were analyzed for their pseudoallergic and pruritogenic effects in mice and human. RESULTS: We found a class of commonly used drugs activating MRGPRX2 that, to a large extent, consists of antidepressants, antiallergic drugs, and antipsychotics. Three-dimensional pharmacophore modeling revealed structural similarities of the identified agonists, classifying them as cationic amphiphilic drugs. Mast cell activation was investigated by using the 3 representatively selected antidepressants clomipramine, paroxetine, and desipramine. Indeed, we were able to show a concentration-dependent activation and MRGPRX2-dependent degranulation of the human mast cell line LAD2 (Laboratory of Allergic Diseases-2). Furthermore, clomipramine, paroxetine, and desipramine were able to induce degranulation of human skin and murine peritoneal mast cells. These substances elicited dose-dependent scratching behavior following intradermal injection into C57BL/6 mice but less so in MRGPRB2-mutant mice, as well as wheal-and-flare reactions following intradermal injections in humans. CONCLUSION: Our results contribute to the characterization of structure-activity relationships and functionality of MRGPRX2 ligands and facilitate prediction of adverse reactions such as drug-induced pruritus to prevent severe drug hypersensitivity reactions.

Directed Dehydration as Synthetic Tool for Generation of a New Na4 SnS4 Polymorph: Crystal Structure, Na+ Conductivity, and Influence of Sb-Substitution.

We present the convenient synthesis and characterization of the new ternary thiostannate Na4 SnS4 (space group I 4 1 / a c d ) by directed removal of crystal water molecules from Na4 SnS4 ⋅14 H2 O. The compound represents a new kinetically stable polymorph of Na4 SnS4 , which is transformed into the known, thermodynamically stable form (space group P 4 ‾ 2 1 c ) at elevated temperatures. Thermal co-decomposition of mixtures with Na3 SbS4 ⋅9 H2 O generates solid solution products Na4-x Sn1-x Sbx S4 (x=0.01, 0.10) isostructural to the new polymorph (x=0). Incorporation of Sb5+ affects the bonding and local structural situation noticeably evidenced by X-ray diffraction, 119 Sn and 23 Na NMR, and 119 Sn Mössbauer spectroscopy. Electrochemical impedance spectroscopy demonstrates an enormous improvement of the ionic conductivity with increasing Sb content for the solid solution (σ25°C =2×10-3 , 2×10-2 , and 0.1 mS cm-1 for x=0, 0.01, and 0.10), being several orders of magnitude higher than for the known Na4 SnS4 polymorph.

Small-Molecular-Weight Additives Modulate Calcification by Interacting with Prenucleation Clusters on the Molecular Level.

Small-molecular-weight (MW) additives can strongly impact amorphous calcium carbonate (ACC), playing an elusive role in biogenic, geologic, and industrial calcification. Here, we present molecular mechanisms by which these additives regulate stability and composition of both CaCO3 solutions and solid ACC. Potent antiscalants inhibit ACC precipitation by interacting with prenucleation clusters (PNCs); they specifically trigger and integrate into PNCs or feed PNC growth actively. Only PNC-interacting additives are traceable in ACC, considerably stabilizing it against crystallization. The selective incorporation of potent additives in PNCs is a reliable chemical label that provides conclusive chemical evidence that ACC is a molecular PNC-derived precipitate. Our results reveal additive-cluster interactions beyond established mechanistic conceptions. They reassess the role of small-MW molecules in crystallization and biomineralization while breaking grounds for new sustainable antiscalants.

Tailored Solution-Based N-heterotriangulene Thin Films: Unravelling the Self-Assembly.

The ability of a series of bridged triarylamines, so-called N-heterotriangulenes, to form multilayer-type 2D-extended films via a solution-based processing method was examined using complementary microscopic techniques. We found that the long-range order, crystallinity, and layer thickness decisively depend on the nature of the substituents attached to the polycyclic backbone. Owing to their flat core unit, compounds exhibiting a carbonyl unit at the bridge position provide a superior building block as compared to thioketone-bridged derivatives. In addition, nature and length of the peripheral substituents affect the orientation of the aromatic core unit within highly crystalline films. Hence, our results stress the significance of a suitable molecular framework and provide deeper understanding of structure formation in 2D-confined surroundings for such compounds.

An embedded atom model for Ga-Pd systems: From intermetallic crystals to liquid alloys.

We present an embedded atom model (EAM) potential for modeling Ga-Pd interactions within intermetallic solids and liquid alloys. The molecular mechanics potential was parameterized on the basis of the structure and mechanical properties of GaPd2, whereas a series of other GaxPd1-x phases and liquid alloy systems allowed rigorous benchmarking. For the intermetallic solids, structures and elastic moduli were found in very reasonable agreement with experimental structures and results from DFT calculations. The liquid models were characterized from molecular dynamics simulations that also showed nice agreement with experimental and ab initio reference data. Moreover, the perspectives of the EAM model are illustrated by the elucidation of an alloy nanodroplet model whose characterization includes the kinetics of Pd dopant diffusion from the Ga droplet surface to the bulk liquid and vice versa.

Mixed Organic Ligand Shells: Controlling the Nanoparticle Surface Morphology toward Tuning the Optoelectronic Properties.

Precise control over the ratio of perylene bisimide (PBI) monomers and aggregates, immobilized on alumina nanoparticle (NP) surfaces, is demonstrated. Towards this goal, phosphonic acid functionalized PBI derivatives (PA-PBI) are shown to self-assemble into stoichiometrically mixed monolayers featuring aliphatic, glycolic, or fluorinated phosphonic acid ligands, serving as imbedding matrix (PA-M) to afford core-shell NPs. Different but, nevertheless, defined PBI monomer/aggregate composition is achieved by either the variation in the PA-PBI to PA-M ratios, or the utilization of different PA-Ms. Various steady-state as well as time-resolved spectroscopy techniques are applied to probe the core-shell NPs with respect to changes in their optical properties upon variations in the shell composition. To this end, the ratio between monomer and excimer-like emission assists in deriving information on the self-assembled monolayer composition, local ordering, and corresponding aggregate content. With the help of X-ray reflectivity measurements, accompanied by molecular dynamics simulations, the built-up of the particle shells, in general, and the PBI aggregation behavior, in particular, are explored in depth.

Approaching Dissolved Species in Ammonoacidic GaN Crystal Growth: A Combined Solution NMR and Computational Study.

Solutions of gallium trihalides GaX3 (X=F, Cl, Br, I) and their ammoniates in liquid ammonia were studied at ambient temperature under autogenous pressure by multinuclear (71 Ga, 35 Cl, 81 Br) NMR spectroscopy. To unravel the role of pH, the analyses were done both in absence and in presence of ammonium halides, which are employed as mineralizers during ammonoacidic gallium nitride crystal growth. While gallium trifluoride and its ammoniate were found to be too sparingly soluble to give rise to a NMR signal, the spectra of solutions of the heavier halides reveal the presence of a single gallium-containing species in all cases. DFT calculations and molecular dynamics simulations suggest the identification of this species as consisting of a [Ga(NH3 )6 ]3+ cation and up to six surrounding halide anions, resulting in an overall trend towards negative complex charge. Quantitative 71 Ga NMR studies on saturated solutions of GaCl3 containing various amounts of additional NH4 Cl revealed a near linear increase of GaCl3 solubility with mineralizer concentration of about 0.023 mol GaCl3 per mol NH4 Cl at room temperature. These findings reflect the importance of Coulombic shielding for the inhibition of oligomerization and precipitation processes and help to rationalize both the low solubility of gallium halides in neutral ammonia solution and, in turn, the proliferating effect of the mineralizer during ammonoacidic gallium nitride formation.

Interface between Water-Solvent Mixtures and a Hydrophobic Surface.

The mechanism behind the stability of organic nanoparticles prepared by liquid antisolvent (LAS) precipitation without a specific stabilizing agent is poorly understood. In this work, we propose that the organic solvent used in the LAS process rapidly forms a molecular stabilizing layer at the interface of the nanoparticles with the aqueous dispersion medium. To confirm this hypothesis, n-octadecyltrichlorosilane (OTS)-functionalized silicon wafers in contact with water-solvent mixtures were used as a flat model system mimicking the solid-liquid interface of the organic nanoparticles. We studied the equilibrium structure of the interface by X-ray reflectometry (XRR) for water-solvent mixtures (methanol, ethanol, 1-propanol, 2-propanol, acetone, and tetrahydrofuran). The formation of an organic solvent-rich layer at the solid-liquid interface was observed. The layer thickness increases with the organic solvent concentration and correlates with the polar and hydrogen bond fraction of Hansen solubility parameters. We developed a self-consistent adsorption model via complementing adsorption isotherms obtained from XRR data with molecular dynamics simulations.

Size-Dependent Local Ordering in Melanin Aggregates and Its Implication on Optical Properties.

We present atomic scale models of differently sized eumelanin nanoaggregates from molecular dynamics simulations combined with a simulated annealing procedure. The analysis reveals the formation of secondary structures due to π-stacking on one hand, but on the other hand a broad distribution of stack geometries in terms of stack size, horizontal displacement angles, and relative torsion angles. The displacement angle distribution, which is a measure of the occurrence of zigzag and linear stacking motives, respectively, strongly depends on the aggregate size-and is hence controlled by the interplay of surface and bulk energy terms. Semiempirical spectra calculations of small stacks (up to five protomolecules) reveal a strong dependence on the precise stack structure and allow for a direct structure-property correlation. The observed spectral shifts result in an overall spectral broadening and, hence, further support the geometric disorder model, which complements the chemical disorder model in the interpretation of eumelanin's monotonically increasing broad-band absorption.

Solvation structure and dynamics of Ag+ in aqueous ammonia solutions: A molecular simulation study.

We present an ab initio-based force-field for silver ion interactions with water and ammonia. Compared to quantum calculations, our model allows for rather large-scale molecular dynamics simulations of silver solutions of aqueous ammonia. For a series of NH3:H2O ratios ranging from 1 to 20 mol. %, Ag+ ions were mainly found as octahedral [Ag(NH3)x(H2O)]6-x+ coordination complexes with preferential values of x ranging from 0 to 3. In the first coordination structure, water ↔ ammonia exchanges occur within a 1-3 ps time scale and, depending on the NH3 concentration, imply significant fluctuations of x covering the whole range from 0 to 6. Based on ns-scale molecular dynamics simulations, chemical potentials are derived for all Ag+ coordination species as functions of temperature and ammonia concentration. Moreover, we compare the diffusion constants of the [Ag(H2O)6]+ to [Ag(H2O)3(NH3)3]+ coordination complexes, based on the solutions of the corresponding ammonia content.

Thermodynamics and Kinetics of Prenucleation Clusters, Classical and Non-Classical Nucleation.

Recent observations of prenucleation species and multi-stage crystal nucleation processes challenge the long-established view on the thermodynamics of crystal formation. Here, we review and generalize extensions to classical nucleation theory. Going beyond the conventional implementation as has been used for more than a century now, nucleation inhibitors, precursor clusters and non-classical nucleation processes are rationalized as well by analogous concepts based on competing interface and bulk energy terms. This is illustrated by recent examples of species formed prior to/instead of crystal nucleation and multi-step nucleation processes. Much of the discussed insights were obtained from molecular simulation using advanced sampling techniques, briefly summarized herein for both nucleation-controlled and diffusion-controlled aggregate formation.