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.

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.

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.

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.

The nano- and meso-scale structure of amorphous calcium carbonate.

Understanding the underlying processes of biomineralization is crucial to a range of disciplines allowing us to quantify the effects of climate change on marine organisms, decipher the details of paleoclimate records and advance the development of biomimetic materials. Many biological minerals form via intermediate amorphous phases, which are hard to characterize due to their transient nature and a lack of long-range order. Here, using Monte Carlo simulations constrained by X-ray and neutron scattering data together with model building, we demonstrate a method for determining the structure of these intermediates with a study of amorphous calcium carbonate (ACC) which is a precursor in the bio-formation of crystalline calcium carbonates. We find that ACC consists of highly ordered anhydrous nano-domains of approx. 2 nm that can be described as nanocrystalline. These nano-domains are held together by an interstitial net-like matrix of water molecules which generate, on the mesoscale, a heterogeneous and gel-like structure of ACC. We probed the structural stability and dynamics of our model on the nanosecond timescale by molecular dynamics simulations. These simulations revealed a gel-like and glassy nature of ACC due to the water molecules and carbonate ions in the interstitial matrix featuring pronounced orientational and translational flexibility. This allows for viscous mobility with diffusion constants four to five orders of magnitude lower than those observed in solutions. Small and ultra-small angle neutron scattering indicates a hierarchically-ordered organization of ACC across length scales that allow us, based on our nano-domain model, to build a comprehensive picture of ACC formation by cluster assembly from solution. This contribution provides a new atomic-scale understanding of ACC and provides a framework for the general exploration of biomineralization and biomimetic processes.

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.

Red light-triggered photoreduction on a nucleic acid template.

Conjugate Sn(iv)(pyropheophorbide a)dichloride-(peptide nucleic acid) catalyzes reduction of azobenzene derivatives in the presence of complementary nucleic acid (NA) upon irridiation with red light (660 nm). This is the first red light-induced NA-templated photoreduction. It is highly sensitive to single mismatches in the NA-template and can detect down to 5 nM NAs.

Hydration breaking and chemical ordering in a levitated NaCl solution droplet beyond the metastable zone width limit: evidence for the early stage of two-step nucleation.

For over two decades, NaCl nucleation from a supersaturated aqueous solution has been predicted to occur via a two-step nucleation (TSN) mechanism, i.e., two sequential events, the formation of locally dense liquid regions followed by structural ordering. However, the formation of dense liquid regions in the very early stage of TSN has never been experimentally observed. By using a state-of-the-art technique, a combination of electrostatic levitation (ESL) and in situ synchrotron X-ray and Raman scatterings, we find experimental evidence that indicates the formation of dense liquid regions in NaCl bulk solution at an unprecedentedly high level of supersaturation (S = 2.31). As supersaturation increases, evolution of ion clusters leads to chemical ordering, but no topological ordering, which is a precursor for forming the dense disordered regions of ion clusters at the early stage of TSN. Moreover, as the ion clusters proceed to evolve under highly supersaturated conditions, we observe the breakage of the water hydration structure indicating the stability limit of the dense liquid regions, and thus leading to nucleation. The evolution of solute clusters and breakage of hydration in highly supersaturated NaCl bulk solution will provide new insights into the detailed mechanism of TSN for many other aqueous solutions.

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.

Molecular mechanisms of mesoporous silica formation from colloid solution: Ripening-reactions arrest hollow network structures.

The agglomeration of silica nanoparticles in aqueous solution is investigated from molecular simulations. Mimicking destabilization of colloidal solutions by full removal of protective moieties or surface charge, association of SiO2/Si(OH)4 core/shell particles leads to rapid proton transfer reactions that account for local silanole → silica ripening reactions. Yet, such virtually barrier-less binding is only observed within a limited contact zone. Agglomeration hence leads to the formation of oligomers of nanoparticles, whilst full merging into a compact precipitate is hampered by the need for extended structural reorganisation. Implementing sufficiently fast supply from colloidal solution, our simulations show the development of silica networks comprised of covalently bound, yet not fully merged nanoparticles. Within the oligomerized nanoparticle network, coordination numbers range from 2 to 5 -which is far below closest packing. Our simulations hence rationalize the formation of covalently bound network structures hosting extended pores. The resulting interfaces to the solvent show water immobilization only for the immediate contact layers, whilst the inner pores exhibit solvent mobility akin to bulk water.

Multi-Scale Modelling of Deformation and Fracture in a Biomimetic Apatite-Protein Composite: Molecular-Scale Processes Lead to Resilience at the µm-Scale.

Fracture mechanisms of an enamel-like hydroxyapatite-collagen composite model are elaborated by means of molecular and coarse-grained dynamics simulation. Using fully atomistic models, we uncover molecular-scale plastic deformation and fracture processes initiated at the organic-inorganic interface. Furthermore, coarse-grained models are developed to investigate fracture patterns at the µm-scale. At the meso-scale, micro-fractures are shown to reduce local stress and thus prevent material failure after loading beyond the elastic limit. On the basis of our multi-scale simulation approach, we provide a molecular scale rationalization of this phenomenon, which seems key to the resilience of hierarchical biominerals, including teeth and bone.

Atomistic modeling of a KRT35/KRT85 keratin dimer: folding in aqueous solution and unfolding under tensile load.

We present an atomistic model of a full KRT35/KRT85 dimer, a fundamental building block of human hair. For both monomers initial structures were generated using empirical tools based on homology considerations, followed by the formulation of a naiïve dimer model from docking the monomers in vacuum. Relaxation in aqueous solution was then explored from molecular dynamics simulation. Driven by hydrophobic segregation and protein-protein hydrogen bonding relaxation dynamics result in a folded dimer arrangement which shows a striking encounter of cystein groups. Our simulations hence suggests that (i) cystein groups in the coil regions of keratin are well suited to establish disulfide bonds between the two monomers that constitute the dimer, and (ii) the particularly large number of cystein groups in the head and tail regions promotes the connection of dimers to establish meso- to macroscale fibers. Moreover, we show the molecular mechanisms of elastic and plastic deformation under tensile load. Upon elongation beyond the elastic regime, unfolding was identified as the exposure of hydrophobic moieties and the breaking of protein-protein hydrogen bonds. Therein, the step-wise character of the series of unfolding events leads to a broad regime of constant force in response to further elongation.

Molecular Mechanisms of ZnO Nanoparticle Dispersion in Solution: Modeling of Surfactant Association, Electrostatic Shielding and Counter Ion Dynamics.

Molecular models of 5 nm sized ZnO/Zn(OH)2 core-shell nanoparticles in ethanolic solution were derived as scale-up models (based on an earlier model created from ion-by-ion aggregation and self-organization) and subjected to mechanistic analyses of surface stabilization by block-copolymers. The latter comprise a poly-methacrylate chain accounting for strong surfactant association to the nanoparticle by hydrogen bonding and salt-bridges. While dangling poly-ethylene oxide chains provide only a limited degree of sterical hindering to nanoparticle agglomeration, the key mechanism of surface stabilization is electrostatic shielding arising from the acrylates and a halo of Na+ counter ions associated to the nanoparticle. Molecular dynamics simulations reveal different solvent shells and distance-dependent mobility of ions and solvent molecules. From this, we provide a molecular rationale of effective particle size, net charge and polarizability of the nanoparticles in solution.

Mimicking the growth of a pathologic biomineral: shape development and structures of calcium oxalate dihydrate in the presence of polyacrylic acid.

The morphogenesis of calcium oxalate hydrates in aqueous solutions was investigated by varying the pH, oxalate concentration, and the concentration of the sodium salt of polyacrylate (PAA). With increasing amounts of PAA in solution, the shape of tetragonal calcium oxalate dihydrate (COD) changes from bipyramidal through elongated bipyramidal prisms to dumbbells and finally reverts to rodlike tetragonal bipyramidal prisms. PAA is incorporated into the prismatic zones of the growing COD crystals, thereby reducing the growth rate of the {100} faces along the <100> direction. Dumbbells start to develop through "non-crystallographic" branching from the prism faces and the formation of "multiple head" crystals. Adsorption of PAA on the rough surfaces of the splitting individuals supports the selection of new subindividuals and leads to the formation of core-shell patterns. The various shapes and structures of the biomimetic COD/PAA crystals and aggregates are closely related to the well-known "pathologic" individuals observed in the urine of patients with urinary disease (including urinary stones).

Molecular mechanics modeling of azobenzene-based photoswitches.

We present an extension of the generalized amber force field to allow the modeling of azobenzenes by means of classical molecular mechanics. TD-DFT calculations were employed to derive different interaction models for 4-hydroxy-4'-methyl-azobenzene, including the ground (S(0)) and S(1) excited state. For both states, partial charges and the -N = N- torsion potentials were characterized. On this basis, we pave the way to large-scale model simulations involving azobenzene molecular switches. Using the example of an isolated molecule, the mechanics of cyclic switching processes are demonstrated by classical molecular dynamics simulations.

Atomistic modeling of apatite-collagen composites from molecular dynamics simulations extended to hyperspace.

The preparation of atomistic models of apatite-collagen composite mimicking enamel at length scales in the range of 1-10 nanometers is outlined. This bio-composite is characterized by a peculiar interplay of the collagen triplehelix and the apatite crystal structure. Structural coherence is however only obtained after drastic rearrangements, namely the depletion of protein-protein hydrogen bonds and the incorporation of calcium triangles which are stabilized by salt-bridges with the collagen molecule. Starting from an isolated collagen triple helix and a single-crystalline apatite structure, a composite model is obtained by gradually merging the two components via an additional (hyperspace) coordinate. This approach allows smooth structural relaxation of both components whilst avoiding singularities in potential energy due to atomic overlap.

Motif reconstruction in clusters and layers: benchmarks for the Kawska-Zahn approach to model crystal formation.

A recently developed atomistic simulation scheme for investigating ion aggregation from solution is transferred to the morphogenesis of metal clusters grown from the vapor and layers deposited on a substrate surface. Both systems are chosen as benchmark models for intense motif reorganization during aggregate/layer growth. The applied simulation method does not necessarily involve global energy minimization after each growth event, but instead describes crystal growth as a series of structurally related configurations which may also include local energy minima. Apart from the particularly favorable high-symmetry configurations known from experiments and global energy minimization, we also demonstrate the investigation of transient structures. In the spirit of Ostwald's step rule, a continuous evolution of the aggregate/layer structure during crystal growth is observed.

Atomistic mechanisms of ZnO aggregation from ethanolic solution: ion association, proton transfer, and self-organization.

We report on atomistic simulations related to the nucleation of zinc oxide nanocrystals from ethanolic solution. The underlying mechanisms are explored from the very initial stage of Zn2+ and OH(-) ion association to the formation of nanometer-sized aggregates counting up to 250 ions. The embryonic aggregates consist of zinc and hydroxide ions, only. At later stages of aggregate growth, proton transfer reactions at the aggregate-solvent interface account for the formation of O(2-) ions and induce the precipitation of zinc oxide. After the association of around 150 ions, ZnO domains were found to nucleate in the central region of the [Znx(OH)yOz]2x-y-2z) aggregates. In the course of further ion association and condensation reactions, progressive self-organization leads to an extended core in which the ions are arranged according to the wurtzite structure.