Significance of atomic-scale defects in flexible surfaces on local solvent and ion behaviour.

Many factors can affect the course of heterogeneous nucleation, such as surface chemistry, flexibility and topology, substrate concentration and solubility. Atomic-scale defects are rarely investigated in detail and are often considered to be unimportant surface features. In this work, we set out to investigate the significance of atomic-scale defects in a flexible self-assembled monolayer surface for the behaviour of clusters of Ca2+ and CO32- ions in water. To this end, we use molecular dynamics simulations to estimate the diffusion coefficients of ion clusters at different topological surface features and obtain ionic radial distribution functions around features of interest. Well-tempered metadynamics is used to gain insight into the free energy of ions around selected surface defects. We find that certain defects, which we refer to as active defects, can impair ionic surface diffusion, as well as affect the diffusion of ions in close proximity to the surface feature in question. Our findings suggest that this effect can result in an ability of such topological features to promote ion clustering and increase local ionic concentration at specific surface sites. The work reported here shows how the presence of small atomic-scale defects can affect the role of a surface in the process of heterogeneous nucleation and contributes towards a rational definition of surfaces as effective nucleating agents.

A general method for calculating solid/liquid interfacial free energies from atomistic simulations: Application to CaSO4·xH2O.

We present a general method for computing interfacial free energies from atomistic simulations, which is particularly suitable for solid/liquid interfaces. Our method uses an Einstein crystal as a universal reference state and is more flexible than previous approaches. Surfaces with dipoles, complex reconstructions, and miscible species are all easily accommodated within the framework. It may also be extended to calculating the relative free energies of different phases and other types of defect. We have applied our method to interfaces of bassanite and gypsum with water and obtained interfacial free energies of the order of 0.12 J/m2, of which ∼45% is due to entropic contributions. Our calculations of the interfacial free energy of NaCl with water obtained a value of 0.13 J/m2, of which only 19% is from entropic contributions. We have also predicted equilibrium morphologies for bassanite and gypsum that compare well with experiments and previous calculations.

The Role of Extracellular DNA in Microbial Attachment to Oxidized Silicon Surfaces in the Presence of Ca2+ and Na.

Attachment assays of a Pseudomonas isolate to fused silica slides showed that treatment with DNaseI significantly inhibited cellular adsorption, which was restored upon DNA treatment. These assays confirmed the important role of extracellular DNA (eDNA) adsorption to a surface. To investigate the eDNA adsorption mechanism, single-molecule force spectroscopy (SMFS) was used to measure the adsorption of eDNA to silicon surfaces in the presence of different concentrations of sodium and calcium ions. SMFS reveals that the work of adhesion required to remove calcium-bound eDNA from the silicon oxide surface is substantially greater than that for sodium. Molecular dynamics simulations were also performed, and here, it was shown that the energy gain in eDNA adsorption to a silicon oxide surface in the presence of calcium ions is small and much less than that in the presence of sodium. The simulations show that the length scales involved in eDNA adsorption are less in the presence of sodium ions than those in the presence of calcium. In the presence of calcium, eDNA is pushed above the surface cations, whereas in the presence of sodium ions, short-range interactions with the surface dominate. Moreover, SMFS data show that increasing [Ca2+] from 1 to 10 mM increases the adsorption of the cations to the silicon oxide surface and consequently enhances the Stern layer, which in turn increases the length scale associated with eDNA adsorption.

Ion Association in Lanthanide Chloride Solutions.

A better understanding of the solution chemistry of the lanthanide (Ln) salts in water would have wide ranging implications in materials processing, waste management, element tracing, medicine and many more fields. This is particularly true for minerals processing, given governmental concerns about lanthanide security of supply and the drive to identify environmentally sustainable processing routes. Despite much effort, even in simple systems, the mechanisms and thermodynamics of LnIII association with small anions remain unclear. In the present study, molecular dynamics (MD), using a newly developed force field, provide new insights into LnCl3 (aq) solutions. The force field accurately reproduces the structure and dynamics of Nd3+ , Gd3+ and Er3+ in water when compared to calculations using density functional theory (DFT). Adaptive-bias MD simulations show that the mechanisms for ion pairing change from dissociative to associative exchange depending upon cation size. Thermodynamics of association reveal that whereas ion pairing is favourable, the equilibrium distribution of species at low concentration is dominated by weakly bound solvent-shared and solvent-separated ion pairs, rather than contact ion pairs, reconciling a number of contrasting observations of LnIII -Cl association in the literature. In addition, we show that the thermodynamic stabilities of a range of inner sphere and outer sphere LnCl x ( 3 - x ) + coordination complexes are comparable and that the kinetics of anion binding to cations may control solution speciation distributions beyond ion pairs. The techniques adopted in this work provide a framework with which to investigate more complex solution chemistries of cations in water.

Tuning hardness in calcite by incorporation of amino acids.

Structural biominerals are inorganic/organic composites that exhibit remarkable mechanical properties. However, the structure-property relationships of even the simplest building unit-mineral single crystals containing embedded macromolecules-remain poorly understood. Here, by means of a model biomineral made from calcite single crystals containing glycine (0-7 mol%) or aspartic acid (0-4 mol%), we elucidate the origin of the superior hardness of biogenic calcite. We analysed lattice distortions in these model crystals by using X-ray diffraction and molecular dynamics simulations, and by means of solid-state nuclear magnetic resonance show that the amino acids are incorporated as individual molecules. We also demonstrate that nanoindentation hardness increased with amino acid content, reaching values equivalent to their biogenic counterparts. A dislocation pinning model reveals that the enhanced hardness is determined by the force required to cut covalent bonds in the molecules.

The Effect of Additives on the Early Stages of Growth of Calcite Single Crystals.

As crystallization processes are often rapid, it can be difficult to monitor their growth mechanisms. In this study, we made use of the fact that crystallization proceeds more slowly in small volumes than in bulk solution to investigate the effects of the soluble additives Mg2+ and poly(styrene sulfonate) (PSS) on the early stages of growth of calcite crystals. Using a "Crystal Hotel" microfluidic device to provide well-defined, nanoliter volumes, we observed that calcite crystals form via an amorphous precursor phase. Surprisingly, the first calcite crystals formed are perfect rhombohedra, and the soluble additives have no influence on the morphology until the crystals reach sizes of 0.1-0.5 µm for Mg2+ and 1-2 µm for PSS. The crystals then continue to grow to develop morphologies characteristic of these additives. These results can be rationalized by considering additive binding to kink sites, which is consistent with crystal growth by a classical mechanism.

How does an amorphous surface influence molecular binding?--ovocleidin-17 and amorphous calcium carbonate.

Atomistic molecular dynamics simulations of dehydrated amorphous calcium carbonate interacting with the protein ovocleidin-17 are presented. These simulations demonstrate that the amorphisation of the calcium carbonate surface removes water structure from the surface. This reduction of structure allows the protein to bind with many residues, unlike on crystalline surfaces where binding is strongest when only a few residues are attached to the surface. Basic residues are observed to dominate the binding interactions. The implications for protein control over crystallisation are discussed.

Adsorption of poly acrylic acid onto the surface of calcite: an experimental and simulation study.

Macromolecular binding to minerals is of great importance in the formation of biofilms, and carboxylate functional groups have been found to play a pivotal role in the functioning of these macromolecules. Here we present both fluorescence time-resolved anisotropy measurements and simulation data on the conformational behaviour and binding of a poly acrylic acid polymer. In solution the polymer exhibits a pH dependent behaviour, with a coiled conformation at a low pH and extended conformation at higher pH values. The polymer is readily adsorbed on the surface of calcite, preferring to bind in an extended conformation, with the strength of the adsorption dependent on the pH and presence of counter ions. We discuss the reasons why the calculated adsorption free energy differs from that obtained from a Langmuir isotherm analysis, showing that they refer to different quantities. The enhanced binding of the extended conformations shows the importance of flexibility in the binding of macromolecules.

Dynamic tilting in perovskites.

A new computational analysis of tilt behaviour in perovskites is presented. This includes the development of a computational program - PALAMEDES - to extract tilt angles and the tilt phase from molecular dynamics simulations. The results are used to generate simulated selected-area electron and neutron diffraction patterns which are compared with experimental patterns for CaTiO3. The simulations not only reproduced all symmetrically allowed superlattice reflections associated with tilt but also showed local correlations that give rise to symmetrically forbidden reflections and the kinematic origin of diffuse scattering.

Electron transparent nanotubes reveal crystallization pathways in confinement.

The cylindrical pores of track-etched membranes offer excellent environments for studying the effects of confinement on crystallization as the pore diameter is readily varied and the anisotropic morphologies can direct crystal orientation. However, the inability to image individual crystals in situ within the pores in this system has prevented many of the underlying mechanisms from being characterized. Here, we study the crystallization of calcium sulfate within track-etched membranes and reveal that oriented gypsum forms in 200 nm diameter pores, bassanite in 25-100 nm pores and anhydrite in 10 nm pores. The crystallization pathways are then studied by coating the membranes with an amorphous titania layer prior to mineralization to create electron transparent nanotubes that protect fragile precursor materials. By visualizing the evolutionary pathways of the crystals within the pores we show that the product single crystals derive from multiple nucleation events and that orientation is determined at early reaction times. Finally, the transformation of bassanite to gypsum within the membrane pores is studied using experiment and potential mean force calculations and is shown to proceed by localized dissolution/reprecipitation. This work provides insight into the effects of confinement on crystallization processes, which is relevant to mineral formation in many real-world environments.