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.

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.

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.

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.

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.

Amino Acid and Oligopeptide Effects on Calcium Carbonate Solutions.

Biological organisms display sophisticated control of nucleation and crystallization of minerals. In order to mimic living systems, deciphering the mechanisms by which organic molecules control the formation of mineral phases from solution is a key step. We have used computer simulations to investigate the effects of the amino acids arginine, aspartic acid, and glycine on species that form in solutions of calcium carbonate (CaCO3) at lower and higher levels of supersaturation. This provides net positive, negative, and neutral additives. In addition, we have prepared simulations containing hexapeptides of the amino acids to consider the effect of additive size on the solution species. We find that additives have limited impact on the formation of extended, liquid-like CaCO3 networks in supersaturated solutions. Additives control the amount of (bi)carbonate in solution, but more importantly, they are able to stabilize these networks on the time scales of the simulations. This is achieved by coordinating the networks and assembled additive clusters in solutions. The association leads to subtle changes in the coordination of CaCO3 and reduced mobility of the cations. We find that the number of solute association sites and the size and topology of the additives are more important than their net charge. Our results help to understand why polymer additives are so effective at stabilizing dense liquid CaCO3 phases.

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.

Simulation of Calcium Phosphate Prenucleation Clusters in Aqueous Solution: Association beyond Ion Pairing.

Classical molecular dynamics simulations and free energy methods have been used to obtain a better understanding of the molecular processes occurring prior to the first nucleation event for calcium phosphate biominerals. The association constants for the formation of negatively charged complexes containing calcium and phosphate ions in aqueous solution have been computed, and these results suggest that the previously proposed calcium phosphate building unit, [Ca(HPO4)3]4-, should only be present in small amounts under normal experimental conditions. However, the presence of an activation barrier for the removal of an HPO4 2- ion from this complex indicates that this species could be kinetically trapped. Aggregation pathways involving CaHPO4, [Ca(HPO4)2]2-, and [Ca(HPO4)3]4- complexes have been explored with the finding that dimerization is favorable up to a Ca/HPO4 ratio of 1:2.

Simulation of Calcium Phosphate Species in Aqueous Solution: Force Field Derivation.

A new force field has been derived for the aqueous calcium phosphate system that aims to reproduce the key thermodynamic properties of the system, including free energies of hydration of the ions and the solubility of the solid mineral phases. Interactions of three phosphate anions (PO43-, HPO42-, and H2PO4-) with water were calibrated through comparison with the results obtained from ab initio molecular dynamics using both GGA and hybrid density functional theory with dispersion corrections. In the solid state, the force field has been evaluated by benchmarking against experiment and other existing models and is shown to reproduce the structural and mechanical properties well, despite the primary focus being on thermodynamics. To validate the force field, the thermodynamics of ion pairing for calcium phosphate species in water has been computed and shown to be in excellent agreement with experimental data.

The role of extracellular DNA in uranium precipitation and biomineralisation.

Bacterial extra polymeric substances (EPS) have been associated with the extracellular precipitation of uranium. Here we report findings on the biomineralisation of uranium, with extracellular DNA (eDNA) used as a model biomolecule representative of EPS. The complexation and precipitation of eDNA with uranium were investigated as a function of pH, ionic strength and varying concentrations of reactants. The role of phosphate moieties in the biomineralisation mechanism was studied by enzymatically releasing phosphate (ePO4) from eDNA compared to abiotic phosphate (aPO4). The eDNA-uranium precipitates and uranium minerals obtained were characterised by Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FT-IR) spectroscopy, Scanning Electron Microscopy-Energy Dispersive X-Ray analysis (SEM-EDX), X-Ray Powder Diffraction (XRD) and X-Ray Photoelectron Spectroscopy (XPS). ATR-FT-IR showed that at pH 5, the eDNA-uranium precipitation mechanism was predominantly mediated by interactions with phosphate moieties from eDNA. At pH 2, the uranium interactions with eDNA occur mainly through phosphate. The solubility equilibrium was dependent on pH with the formation of precipitate reduced as the pH increased. The XRD data confirmed the formation of a uranium phosphate precipitate when synthesised using ePO4. XPS and SEM-EDX studies showed the incorporation of carbon and nitrogen groups from the enzymatic orthophosphate hydrolysis on the obtained precipitated. These results suggested that the removal of uranium from solution occurs via two mechanisms: complexation by eDNA molecules and precipitation of a uranium phosphate mineral of the type (UO2HPO4)·xH2O by enzymatic orthophosphate hydrolysis. This demonstrated that eDNA from bacterial EPS is a key contributor to uranium biomineralisation.

Protein sequences bound to mineral surfaces persist into deep time.

Proteins persist longer in the fossil record than DNA, but the longevity, survival mechanisms and substrates remain contested. Here, we demonstrate the role of mineral binding in preserving the protein sequence in ostrich (Struthionidae) eggshell, including from the palaeontological sites of Laetoli (3.8 Ma) and Olduvai Gorge (1.3 Ma) in Tanzania. By tracking protein diagenesis back in time we find consistent patterns of preservation, demonstrating authenticity of the surviving sequences. Molecular dynamics simulations of struthiocalcin-1 and -2, the dominant proteins within the eggshell, reveal that distinct domains bind to the mineral surface. It is the domain with the strongest calculated binding energy to the calcite surface that is selectively preserved. Thermal age calculations demonstrate that the Laetoli and Olduvai peptides are 50 times older than any previously authenticated sequence (equivalent to ~16 Ma at a constant 10°C).

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.

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.

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.

Order parameter and connectivity topology analysis of crystalline ceramics for nuclear waste immobilization.

We apply bond order and topological methods to the problem of analysing the results of radiation damage cascade simulations in ceramics. Both modified Steinhardt local order and connectivity topology analysis techniques provide results that are both translationally and rotationally invariant and which do not rely on a particular choice of a reference structure. We illustrate the methods with new analyses of molecular dynamics simulations of single cascades in the pyrochlores Gd(2)Ti(2)O(7) and Gd(2)Zr(2)O(7) similar to those reported previously (Todorov et al 2006 J. Phys.: Condens. Matter 18 2217). Results from the Steinhardt and topology analyses are consistent, while often providing complementary information, since the Steinhardt parameters are sensitive to changes in angular arrangement even when the overall topological connectivity is fixed. During the highly non-equilibrium conditions at the start of the cascade, both techniques reveal significant localized transient structural changes and variation in the cation connectivity. After a few picoseconds, the connectivity is largely fixed, while the order parameters continue to change. In the zirconate there is a shift to the anion disordered system while in the titanate there is substantial reversion and healing back to the parent pyrochlore structure.

The Development of a Classical Force Field To Determine the Selectivity of an Aqueous Fe(3+)-EDA Complex for TcO4(-) and SO4(2.).

A classical force field has been developed in order to investigate the selective exchange of oxyanions (TcO4(-) vs SO4(2-)) with other ligands (H2O, Cl(-)) to an aqueous Fe(3+)-ethylenediamine (EDA) complex. Potentials of mean force for a range of exchange reactions were generated using umbrella sampling and classical molecular dynamics simulations in order to calculate the affinity of each oxyanion for the Fe(3+)-EDA complex in aqueous solution. In order to accurately introduce a degree of specificity for the interaction of Fe(3+) with each ligand type, force field parameters were tuned to match the results of density functional theory calculations. Preferential exchange of H2O, Cl(-), and SO4(2-) for TcO4(-) via an interchange mechanism is observed, in agreement with experimental observations. Both the relative solvation entropies and enthalpies of the anions were found to be critically important factors governing the magnitude of the observed selectivities. These results have important implications for the design and modeling of functionalized materials for the remediation of land contaminated with radioactive (99)Tc.

A computational investigation of nickel (silicides) as potential contact layers for silicon photovoltaic cells.

Nickel has been proposed as a low-cost alternative to silver for contacting in high-performance solar cells. Nickel at a crystalline silicon surface can form a number of silicide phases, depending on fabrication conditions. Using density functional theory calculations we calculate the Schottky barrier height (SBH) at the different possible interfaces. Depending on the silicide phase, crystallographic orientation and doping the SBH at the interface with Si can range from 0.39 to 0.70 eV. These calculations demonstrate which of the nickel (silicide) phases have potential use as contacting materials for silicon based solar cells. Furthermore, we explain the origin of the SBH tuning effect of P dopant atoms as being due to a dipole formed at the interface, demonstrating the linear relationship between the charge transfer at the interface upon doping and the concomitant modulation of the SBH.

Protein binding on stepped calcite surfaces: simulations of ovocleidin-17 on calcite {31.16} and {31.8}.

Simulations using classical molecular dynamics are reported on the binding of the protein Ovocleidin-17 to calcite stepped surfaces. vicinal surfaces ({31.8} and {31.16}) are used to obtain acute and obtuse steps. The simulations demonstrate that binding is greater at the obtuse step. A range of analytical methods is used to show the importance of surface and local water structure for protein binding. We discuss the general features of molecular binding in the light of these results. Our analysis shows that it is unlikely that Ovocleidin-17 is important in controlling crystal morphology; its main role is likely to be in controlling calcite nucleation.

A demonstration of the inhomogeneity of the local dielectric response of proteins by molecular dynamics simulations.

The dielectric properties of proteins are important in determining responses to changes in pH, responses to external electric fields, and the energy associated with charge injection or charge transfer. Although the importance of electrostatic interactions in proteins is well established and they are routinely included in simulations, the dielectric properties of proteins are less frequently discussed. We use a combination of atomistic molecular dynamics simulation and continuum electrostatics models to calculate the local dielectric constant within regions of the model protein hen egg white lysozyme. The local dielectric response of the protein was found to be highly inhomogeneous and strongly dependent on the local chemical environment. In light of these findings, we discuss the use of models using a single effective dielectric constant for the whole protein and the relationship between variations in local protein dielectric response and the activity of protein sites.