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Abstract Solution‐based atomic layer deposition (sALD) is an emerging technique that transfers the principle of traditional atomic layer deposition (ALD) from the gas phase into a wet chemical environment. This new preparation technique has new and unique properties and requirements. A large number of new surfaces and reactants are available to produce active 2D materials. In this work a reproducible procedure to coat silicon wafers with a densely packed monolayer of (3‐Mercaptopropyl)trimethoxysilane (MPTMS) molecules is presented. These highly functionalized surfaces can be used to seed the nucleation of SnS2 in a solution‐based ALD procedure. A coating routine for the production of SnS2 is adapted from ALD to sALD and insight into the nucleation behavior of the reactands is given. X‐ray reflectometry (XRR) is used to resolve the nucleation process of SnS2 on an MPTMS self assembled monolayer (SAM) during the first three cycles of an sALD procedure. The comparison of ex situ XRR, in situ XRR, grazing incidence wide‐angle X‐ray scattering (GIWAXS), atomic force microscopy (AFM), energy dispersive X‐ray spectroscopy (EDX) measurements, and density functional theory (DFT) calculations find that SnS2 first forms a closed layer and then continues to grow in islands on thiol functionalized silane SAMs. Subsequent coating cycles will continue the growth of the islands laterally and in height.

Abstract Responsive chiral systems have attracted considerable attention, given their potential for diverse applications in biology, optoelectronics, photonics, and related fields. Here we show the reversible chirality inversion of an AuAg x -cysteine (AuAg x -cys) coordination polymer (CP) by pH changes. The polymer can be obtained by mixing HAuCl4 and AgNO3 with L-cysteine (or D-cysteine) in appropriate proportions in H2O (or other surfactant solutions). Circular dichroism (CD) spectrum is used to record the strong optical activity of the AuAg0.06-L-cys enantiomer (denoted as L0.06), which can be switched to that of the corresponding D0.06 enantiomer by alkalization (final dispersion pH > 13) and can be switched back after neutralization (final dispersion pH

We combine the charge equilibration (QEq) method with the modified embedded atom model (MEAM) to describe a series of intermetallic GaxPdy compounds at near DFT accuracy. Apart from structure, energetics and elastic properties, a particular focus is dedicated to the partial charges on Ga and Pd sites in the bulk and on flat/terraced surfaces. By the example of GaPd2, we suggest a computationally very efficient approach to assessing the crystal faces and steps of interesting prospect for catalytic activity. To this end, we suggest enhanced catalytic activity of (010) faces by our simulation models that demonstrate particularly large charge transfer between surface Ga and Pd species, namely +0.8 and −0.4, whereas for the (100) and (001) faces local polarization is less than +0.6 and −0.3, respectively. Moreover, the study of rough surfaces is demonstrated from a small series of 10 nm sized simulation models featuring terraces. Local polarization of the atoms at the steps ranges from +0.5 to +1.1 and −0.5 to −0.3 for the Ga and Pd species, respectively.

Abstract 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.

We review approaches to deriving mechanical properties from atomic simulations with a special emphasis on temperature-dependent characterization of polymer materials. The complex molecular network of such materials implies only partial, rather local ordering stemming from the entanglement of molecular moieties or covalent bonding of network nodes, whereas the polymer strands between the nodes may undergo nm-scale reorganization during thermal fluctuations. This not only leads to a strong temperature-dependence of the elastic moduli, but also gives rise to visco-elastic behavior that complicates characterization from molecular dynamics simulations. Indeed, tensile-testing approaches need rigorous evaluation of strain-rate dependences, provoking significant computational demands. Likewise, the use of fluctuations observed from unbiased constant-temperature, constant-pressure molecular dynamics simulation is not straight-forward. However, we suggest pre-processing from Fourier-filtering prior to taking Boltzmann-statistics to discriminate elastic-type vibrations of the simulation models for suitable application of linear-response theory.

Abstract Water boiling control evolution of natural geothermal systems is widely exploited in industrial processes due to the unique non-linear thermophysical behavior. Even though the properties of water both in the liquid and gas state have been extensively studied experimentally and by numerical simulations, there is still a fundamental knowledge gap in understanding the mechanism of the heterogeneous nucleate boiling controlling evaporation and condensation. In this study, the molecular mechanism of bubble nucleation at the hydrophilic and hydrophobic solid–water interface was determined by performing unbiased molecular dynamics simulations using the transition path sampling scheme. Analyzing the liquid to vapor transition path, the initiation of small void cavities (vapor bubbles nuclei) and their subsequent merging mechanism, leading to successively growing vacuum domains (vapor phase), has been elucidated. The molecular mechanism and the boiling nucleation sites’ location are strongly dependent on the solid surface hydrophobicity and hydrophilicity. Then simulations reveal the impact of the surface functionality on the adsorbed thin water molecules film structuring and the location of high probability nucleation sites. Our findings provide molecular-scale insights into the computational aided design of new novel materials for more efficient heat removal and rationalizing the damage mechanisms.

Classical nucleation theory (CNT), which was established about 90 years ago, represents the most commonly used theory in describing nucleation processes. For a fluid-to-solid phase transition, CNT states that the solutes in a supersaturated solution reversibly form small clusters. Once a cluster reaches its critical size, it becomes thermodynamically stable and is favored for further growth. One of the most important assumptions of CNT is that the nucleation process is described by one reaction coordinate and all order parameters proceed simultaneously. Recent studies in experiments, computer simulations, and theory have revealed nonclassical features in the early stage of nucleation. In particular, the decoupling of order parameters involved during a fluid-to-solid transition leads to the so-called two-step nucleation mechanism, in which a metastable intermediate phase (MIP) exists in parallel to the initial supersaturated solution and the final crystals. These MIPs can be high-density liquid phases, mesoscopic clusters, or preordered states. In this Special Issue, we focus on the role of the various MIPs in the early stage of crystal nucleation of organic materials, metals and alloys, aqueous solutions, minerals, colloids, and proteins, and thus on various scenarios of nonclassical pathways of crystallization.

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.

A fabrication method of a multifunctional hybrid material is achieved by using the insoluble organic nacre matrix of the Haliotis laevigata shell infiltrated with gelatin as a confined reaction environment. Inside this organic scaffold magnetite nanoparticles (MNPs) are synthesized. The amount of MNPs can be controlled through the synthesis protocol therefore mineral loadings starting from 15 wt % up to 65 wt % can be realized. The demineralized organic nacre matrix is characterized by small-angle and very-small-angle neutron scattering (SANS and VSANS) showing an unchanged organic matrix structure after demineralization compared to the original mineralized nacre reference. Light microscopy and confocal laser scanning microscopy studies of stained samples show the presence of insoluble proteins at the chitin surface but not between the chitin layers. Successful and homogeneous gelatin infiltration in between the chitin layers can be shown. The hybrid material is characterized by TEM and shows a layered structure filled with MNPs with a size of around 10 nm. Magnetic analysis of the material demonstrates superparamagnetic behavior as characteristic for the particle size. Simulation studies show the potential of collagen and chitin to act as nucleators, where there is a slight preference of chitin over collagen as a nucleator for magnetite. Colloidal-probe AFM measurements demonstrate that introduction of a ferrogel into the chitin matrix leads to a certain increase in the stiffness of the composite material.

We explored the functional role of individual otoconia within the otolith system of mammalians responsible for the detection of linear accelerations and head tilts in relation to the gravity vector. Details of the inner structure and the shape of intact human and artificial otoconia were studied using environmental scanning electron microscopy (ESEM), including decalcification by ethylenediaminetetraacetic acid (EDTA) to discriminate local calcium carbonate density. Considerable differences between the rhombohedral faces of human and artificial otoconia already indicate that the inner architecture of otoconia is not consistent with the point group -3m. This is clearly confirmed by decalcified otoconia specimen which are characterized by a non-centrosymmetric volume distribution of the compact 3+3 branches. This structural evidence for asymmetric mass distribution was further supported by light microscopy in combination with a high speed camera showing the movement of single otoconia specimen (artificial specimen) under gravitational influence within a viscous medium (artificial endolymph). Moreover, the response of otoconia to linear acceleration forces was investigated by particle dynamics simulations. Both, time-resolved microscopy and computer simulations of otoconia acceleration show that the dislocation of otoconia include significant rotational movement stemming from density asymmetry. Based on these findings, we suggest an otolith membrane expansion/stiffening mechanism for enhanced response to linear acceleration transmitted to the vestibular hair cells.

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.

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.

We report molecular dynamics simulations of shear in a biomimetic hydroxyapatite-collagen composite. Our model exhibits elastic properties fully dominated by the inorganic component. However, beyond the elastic regime the biomolecules along with the hierarchical nature of the composite account for the formation of structure-inherent slip zones. These accommodate shear without compromising the overall structure and lead to the sliding of intrinsically defined rods at roughly constant restoring force. Upon releasing load, rod displacement is reversible and backcreep is observed as gradual ionic rearrangement in the slip zone, subjected to an activation barrier.

Adhesion-GPCRs provide essential cell-cell and cell-matrix interactions in development, and have been implicated in inherited human diseases like Usher Syndrome and bilateral frontoparietal polymicrogyria. They are the second largest subfamily of seven-transmembrane spanning proteins in vertebrates, but the function of most of these receptors is still not understood. The orphan Adhesion-GPCR GPR126 has recently been shown to play an essential role in the myelination of peripheral nerves in zebrafish. In parallel, whole-genome association studies have implicated variation at the GPR126 locus as a determinant of body height in the human population. The physiological function of GPR126 in mammals is still unknown. We describe a targeted mutation of GPR126 in the mouse, and show that GPR126 is required for embryonic viability and cardiovascular development.

The investigation of the atomistic mechanisms of processes in complex systems constitutes a major challenge to both theory and experiment. While experimental studies offer a wide variety of insights at the macroscopic scale, the atomistic level of detail often remains elusive. On the other hand, molecular simulation approaches may easily achieve microscopic resolution and hence appear particularly suited for detailed mechanistic analyses. However, the computational effort is typically quite considerable and in many cases special simulation strategies are needed to make simulations possible. This review is dedicated to special approaches for tackling the time/length-scale problem inherent to molecular dynamics simulations. Employing these techniques opened a series of new perspectives. The latter are illustrated with the example of recent simulation studies of the atomistic mechanisms involved in complex processes like crystal nucleation, phase transitions and reactions in solution. Along this line, we discuss the reaction mechanisms for He insertion into C60 fullerenes, nucleation events and domain morphogenesis in pressure-induced phase transitions in solids and ion aggregation from solution.