Experimental and Computational Studies of Incorporation of Cyano Transition Metal Complexes in Potassium Chloride Crystals

Experimental and computational studies of the incorporation of hexacyanoferrate(II), hexacyanocobaltate(III), and hexacyanoferrate(III) into potassium chloride crystals are described. The experimental results showed that the extent of incorporation follows the trend, hexacyanoferrate(II) >> hexacyanoferrate(III) > hexacyanocobaltate(III). Computational modelling produced replacement energies that match the experimental trend. The calculated geometry of the incorporated complexes was also found to match well with previous experimental results

Molecular Dynamics Visualization (MDV): Stereoscopic 3D Display of Biomolecular Structure and Interactions Using the Unity Game Engine

Molecular graphics systems are visualization tools which, upon integration into a 3D immersive environment, provide a unique virtual reality experience for research and teaching of biomolecular structure, function and interactions. We have developed a molecular structure and dynamics application, the Molecular Dynamics Visualization tool, that uses the Unity game engine combined with large scale, multi-user, stereoscopic visualization systems to deliver an immersive display experience, particularly with a large cylindrical projection display. The application is structured to separate the biomolecular modeling and visualization systems. The biomolecular model loading and analysis system was developed as a stand-alone C# library and provides the foundation for the custom visualization system built in Unity. All visual models displayed within the tool are generated using Unity-based procedural mesh building routines. A 3D user interface was built to allow seamless dynamic interaction with the model while being viewed in 3D space. Biomolecular structure analysis and display capabilities are exemplified with a range of complex systems involving cell membranes, protein folding and lipid droplets

Can macrocyclic phosphonate molecules inhibit barium sulfate crystallization?

Macrocyclic compounds such as DOTP (1,4,7,10-tetraazacyclododecanetetrakis(methylenephosphonic acid)) and NOTP (1,4,7,-triazacyclononanetri(methylenephosphonic acid)) are found to inhibit precipitation of barium sulfate just as potently as their non-cyclic counterparts depending on the ionisation state of the molecule. Morphologically, DOTP has a more significant influence on the shape of barium sulfate particles formed than NOTP while turbidity results show that NOTP does not significantly affect the induction time observed, unlike DOTP, which does impact the induction time at higher concentrations. Overall, the inhibition of these macrocyclic compounds can be explained by the number of de-protonated phosphonate groups and is not significantly impacted by the presence of the ring. The presence of calcium ions during barium sulfate crystallization lowers the degree of inhibition for both NOTP and DOTP. Molecular modelling showed that an uncomplexed DOTP molecule could lattice match to the barium sulfate lattice but had fewer Ba?Ophos interactions than the equivalent non-macrocyclic molecule. The comparison of uncomplexed with complexed DOTP shows that the final configuration is similar for these two situations, thus in this case it is not the Ba?Ophos interactions but the overall replacement energy that is important

Can Point Defects in Surfaces in Solution be Atomically Resolved by Atomic Force Microscopy?

While the atomic force microscope (AFM) is able to image mineral surfaces in solution with atomic resolution, so far, it has been a matter of debate whether imaging point defects is also possible under these conditions. The difficulties stem from the limited knowledge of what types of defects may be stable in the presence of an AFM tip, as well as from the complicated imaging mechanism involving interactions between hydration layers over the surface and around the tip apex. Here, we present atomistic molecular dynamics and free energy calculations of the AFM imaging of vacancies and ionic substitutions in the calcite (10-14) surface in water, using a new silica AFM tip model. Our results indicate that both calcium and carbonate vacancies, as well as a magnesium substitution, could be resolved in an AFM experiment, albeit with different imaging mechanisms

Atomistic simulation of the measurement of mechanical properties of gold nanorods by AFM

Mechanical properties of nanoscale objects can be measured with an atomic force microscope (AFM) tip. However, the continuum models typically used to relate the force measured at a certain indentation depth to quantities such as the elastic modulus, may not be valid at such small scales, where the details of atomistic processes need to be taken into account. On the other hand, molecular dynamics (MD) simulations of nanoindentation, which can offer understanding at an atomistic level, are often performed on systems much smaller than the ones studied experimentally. Here, we present large scale MD simulations of the nanoindentation of single crystal and penta-twinned gold nanorod samples on a silicon substrate, with a spherical diamond AFM tip apex. Both the sample and tip sizes and geometries match commercially available products, potentially linking simulation and experiment. Different deformation mechanisms, involving the creation, migration and annihilation of dislocations are observed depending on the nanorod crystallographic structure and orientation. Using the Oliver-Pharr method, the Young's moduli of the (100) terminated and (110) terminated single crystal nanorods, and the penta-twinned nanorod, have been determined to be 103 +/- 2, 140 +/- 4 and 108 +/- 2 GPa, respectively, which is in good agreement with bending experiments performed on nanowires.Peer reviewe

Understanding the mechanism by which nitrilotriacetic acid interacts with precipitating barium sulfate

Morphology modifiers can act in many different ways on the precipitating phase. Inhibitors can alter the solution chemistry and thereby change the supersaturation, they may adsorb onto the surface and block growth and agglomeration, they may alter the ritical nucleus and affect nucleation or they may do a combination of these three. revious work showing that nitrilotriacetic acid (NTA) had a significant effect on barium sulfate precipitation has been expanded upon in order to determine the mechanism by which the observed morphology modification occurs. The absence of significant complexation to barium at the pH of the experiment suggests that NTA affects the critical nuclei of the precipitating barium sulfate. This results in the longer induction times observed using nephelometry, and adsorption onto growth features is probably the mechanism of interaction. Molecular modelling shows that NTA adsorption is favourable on terraces and that hydrogen bonding improves the ability of an additive to adsorb. A fundamental nderstanding of the mechanisms by which additives affect crystal growth is essential if new additives, with predictable effect, are to be designed a priori

Atomistic Simulation of Atomic Force Microscopy Imaging of Hydration Layers on Calcite, Dolomite, and Magnesite Surfaces

Advances in atomic force microscopy (AFM) in water have enabled the study of hydration layer structures on crystal surfaces, and in a recent study on dolomite (CaMg(CO3)(2)), chemical sensitivity was demonstrated by observing significant differences in force-distance curves over the calcium and magnesium ions in the surface. Here, we present atomistic molecular dynamics simulations of a hydration layer structure and dynamics on the (10 (1) over bar4) surfaces of dolomite, calcite (CaCO3), and magnesite (MgCO3), as well as simulations of AFM imaging on these three surfaces with a model silica tip. Our results confirm that it should be possible to distinguish between water molecules coordinating the calcium and magnesium ions in dolomite, and the details gleaned from the atomistic simulations enable us to clarify the underlying imaging mechanism in the AFM experiments.Peer reviewe

Understanding barium sulfate precipitation onto stainless steel

This paper investigates the influence of barium sulfate scaling and scaling inhibitors on the electrochemical behaviour of stainless steel. The results of a synchrotron radiation grazing incidence X-ray diffraction (SR-GIXRD) and electrochemical impedance spectroscopy (EIS) study on stainless steel shows that different scaling inhibitors interact uniquely with the substrate when barium sulfate is precipitated on the electrode surface. The main effect of the substrate in the presence of inhibitor is a tendency to form smaller barium sulfate particles. The SR-GIXRD patterns obtained in the presence of the two inhibitors were different to each other and to the control, with the carboxylate showing greater amounts of barite solids precipitated together with iron(III) and (II) sulfate, while the phosphonate showed low amounts of barite solid were precipitated. The presence of iron sulfates on the electrode surface as detected by SR-GIXRD, in the case of NTA, suggests that scaling inhibitors are not alwaysbenign, and can promote the dissolution of iron species from the substrate

Anomalous behaviour within a systematic series of barium sulfate growth modifiers

The generally accepted view that phosphonate derivatives are more potent than the analogous carboxylates as crystal growth modifiers for barium sulfate has been systematically studied by using trifunctional molecules varying from the triphosphonate through to the analogous tricarboxylate; the results suggest that predictions based on simple structural features should be made with caution