Effects of quenching rate on amorphous structures of Cu46Zr54 metallic glass

Metallic glass shows some superior properties different from crystalline, but the nature of amorphous structure and structural change during glass transition have not been completely understood yet. Molecular dynamics simulation provides intuitive insight into the microstructure and properties at atomistic level. Before probing into the microstructures of metallic glass with molecular dynamics (MD) simulation, it is important to obtain amorphous state first. In the current work, we reproduce the process of manufacturing metallic glass in laboratory including the melting, equilibrating and quenching procedure with molecular dynamics simulations. The structure changing at melting point and glass transition temperature are investigated with the different cooling processing. The partial radial distribution function (PRDF) is applied as a criterion to judge the final amorphous state obtained considering the quenching at different cooling rates and the effects of cooling rate on the formation of amorphous structures are further discussed.

The influence of geometry and wall character of pores on the permeation of ions and water through desalination membranes

The transport of water and ions across mimicked nanotube membranes with pseudo atoms is studied using molecular dynamics simulations under equilibrium conditions and hydrostatic pressure. Different pore surface properties are constructed by assigning partial charges on the sites of specified atoms to explore the influence of charges and polarity. The energetics of water and ion transports through the nanopores was calculated to evaluate their filterability to water. The simulation results show that the free energy barriers to water and ion conductions much depend on the charges at the pore entrance and the dipole within the pore. The membranes with hydrophobic pores and negatively charged entrances would be very efficient in the water transport and ion rejection. The charges and dipoles of the pore wall and the aligned dipoles of water molecules in the pore can create a significant force on ions.

Effects of quenching rate on amorphous structures of Cu46Zr54 metallic glass

Metallic glass shows some superior properties different from crystalline, but the nature of amorphous structure and structural change during glass transition have not been completely understood yet. Molecular dynamics simulation provides intuitive insight into the microstructure and properties at atomistic level. Before probing into the microstructures of metallic glass with molecular dynamics (MD) simulation, it is important to obtain amorphous state first. In the current work, we reproduce the process of manufacturing metallic glass in laboratory including the melting, equilibrating and quenching procedure with molecular dynamics simulations. The structure changing at melting point and glass transition temperature are investigated with the different cooling processing. The partial radial distribution function (PRDF) is applied as a criterion to judge the final amorphous state obtained considering the quenching at different cooling rates and the effects of cooling rate on the formation of amorphous structures are further discussed.

Modeling of enzyme–substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10

The matrix metalloproteases (MMPs) and the ADAMs (A Disintegrin And Metalloprotease domain) are proteolytic enzyme families containing a catalytic zinc ion, that are implicated in a variety of normal and pathological processes involving tissue remodeling and cancer. Synthetic MMP inhibitors have been designed for applications in pathological situations. However, a greater understanding of substrate binding and the catalytic mechanism is required so that more effective and selective inhibitors may be developed for both experimental and clinical purposes. By modeling a natural substrate spanning P4-P4‘ in complex with the catalytic domains, we aim to compare substrate-specificities between Stromelysin-1 (MMP-3), ADAM-9 and ADAM–10, with the aid of molecular dynamics simulations. Our results show that the substrate retains a favourable antiparallel beta-sheet conformation on the P-side in addition to the well-known orientation of the P'-region of the scissile bond, and that the primary substrate selectivity is dominated by the sidechains in the S1' pocket and the S2/S3 region. ADAM-9 has a hydrophobic residue as the central determinant in the S1' pocket, while ADAM-10 has an amphiphilic residue, which suggests a different primary specificity. The S2/S3 pocket is largely hydrophobic in all three enzymes. Inspired by our molecular dynamics calculations and supported by a large body of literature, we propose a novel, hypothetical, catalytic mechanism where the Zn-ion polarizes the oxygens from the catalytic glutamate to form a nucleophile, leading to a tetrahedral oxyanion anhydride transition state.

Recent progress in the development and use of organic ionic plastic crystal electrolytes

Significant progress has been made recently in the development of Organic Ionic Plastic Crystals (OIPCs), a unique family of solid state electrolytes with applications in electrochemical devices such as lithium batteries and dye-sensitised solar cells. The negligible volatility of OIPCs renders them more suitable than molecular species for long-term device use, while the high thermal and electrochemical stability of many OIPCs fulfils an essential requirement for solid state electrolytes for many device applications. However, the complex mechanisms of conduction through these materials, both in their pure state and in the presence of a small amount of a second component (such as lithium salts to enable their use in lithium batteries) are still not fully understood. At the same time, the range of anions and cations utilised in the synthesis of plastic crystal phases continues to increase. This perspective concentrates on recent research into both fundamental and device-oriented aspects of these materials. Important fundamental understanding of the physical properties and transport mechanisms of different OIPCs has been achieved through use of techniques including variable temperature solid-state NMR and crystallographic analysis, as well as detailed molecular dynamics simulations. In parallel, the applicability of these materials as electrolytes for dye-sensitised solar cells and lithium batteries is being more widely demonstrated. The possibility of using OIPCs as solid state electrolytes for fuel cells is also discussed.

First-principles based force-field for the interaction of proteins with Au(100)(5 x 1): an extension of GolP-CHARMM

Noncovalent recognition between peptides and inorganic materials is an established phenomenon. Key to exploiting these interactions in a wide range of materials self-assembly applications would be to harness the facet-selective control of peptide binding onto these materials. Fundamental understanding of what drives facet-selectivity in peptide binding is developing, but as yet is not sufficient to enable design of predictable facet-specific sequences. Computational simulation of the aqueous peptide-gold interface, commonly used to understand the mechanisms driving adsorption at an atomic level, has thus far neglected the role that surface reconstruction might play in facet specificity. Here the polarizable GolP-CHARMM suite of force fields is extended to include the reconstructed Au(100) surface. The force field, compatible with the bio-organic force field CHARMM, is parametrized using first-principles data. Our extended force field is tailored to reproduce the heterogeneity of weak chemisorbing N and S species to specific locations in the Au(100)(5 × 1) surface identified from the first-principles calculations. We apply our new model to predict and compare the three-dimensional structure of liquid water at Au(111), Au(100)(1 × 1), and Au(100)(5 × 1) interfaces. Using molecular dynamics simulations, we predict an increased likelihood for water-mediated peptide adsorption at the aqueous-Au(100)(1 × 1) interface compared with the Au(100)(5 × 1) interface. Therefore, our findings suggest that peptide binding can discriminate between the native and reconstructed Au(100) interfaces and that the role of reconstruction on binding at the Au(100) interface should not be neglected. © 2013 American Chemical Society.

Structure of the electrical double layer at aqueous gold and silver interfaces for saline solutions

We report the structure of the electrical double layer, determined from molecular dynamics simulations, for a range of saline solutions (NaCl, KCl, MgCl2 and CaCl2) at both 0.16 and 0.60molkg(-1) on different facets of the gold and silver aqueous interfaces. We consider the Au/Ag(111), native Au/Ag(100) and reconstructed Au(100)(5×1) facets. For a given combination of metallic surface and facet, some variations in density profile are apparent across the different cations in solution, with the corresponding chloride counterion profiles remaining broadly invariant. All density profiles at the higher concentration are predicted to be very similar to their low-concentration counterparts. We find that each electrolyte responds differently to the different metallic surface and facets, particularly those of the divalent metal ions. Our findings reveal marked differences in density profiles between facets for a given metallic interface for both Mg(2+) and Ca(2+), with Na(+) and K(+) showing much less distinction. Mg(2+) was the only ion for which we find evidence of materials-dependent differences in interfacial solution structuring between the Ag and Au.

Binding affinities of amino acid analogues at the charged aqueous titania interface : implications for titania-binding peptides

Despite the extensive utilization of biomolecule-titania interfaces, biomolecular recognition and interactions at the aqueous titania interface remain far from being fully understood. Here, atomistic molecular dynamics simulations, in partnership with metadynamics, are used to calculate the free energy of adsorption of different amino acid side chain analogues at the negatively-charged aqueous rutile TiO2 (110) interface, under conditions corresponding with neutral pH. Our calculations predict that charged amino acid analogues have a relatively high affinity to the titania surface, with the arginine analogue predicted to be the strongest binder. Interactions between uncharged amino acid analogues and titania are found to be repulsive or weak at best. All of the residues that bound to the negatively-charged interface show a relatively stronger adsorption compared with the charge-neutral interface, including the negatively-charged analogue. Of the analogues that are found to bind to the titania surface, the rank ordering of the binding affinities is predicted to be "arginine" > "lysine" ≈ aspartic acid > "serine". This is the same ordering as was found previously for the charge-neutral aqueous titania interface. Our results show very good agreement with available experimental data and can provide a baseline for the interpretation of peptide-TiO2 adsorption data.

Structure and properties of citrate overlayers adsorbed at the aqueous Au(111) interface.

One of the most common means of gold nanoparticle (AuNP) biofunctionalization involves the manipulation of precursor citrate-capped AuNPs via ligand displacement. However, the molecular-level structural characteristics of the citrate overlayer adsorbed at the aqueous Au interface at neutral pH remain largely unknown. Access to atomistic-scale details of these interfaces will contribute much needed insight into how AuNPs can be manipulated and exploited in aqueous solution. Here, the structures of such citrate overlayers adsorbed at the aqueous Au(111) interface at pH 7 are predicted and characterized using atomistic molecular dynamics simulations, for a range of citrate surface densities. We find that the overlayers are disordered in the surface density range considered, and that many of their key characteristics are invariant with surface density. In particular, we predict the overlayers to have 3-D, rather than 2-D, morphologies, with the anions closest to the gold surface being oriented with their carboxylate groups pointing away from the surface. We predict both striped and island morphologies for our overlayers, depending on the citrate surface density, and in all cases we find bare patches of the gold surface are present. Our simulations suggest that both citrate-gold adsorption and citrate-counterion pairing contribute to the stability of these citrate overlayer morphologies. We also calculate the free energy of adsorption at the aqueous Au(111) interface of a single citrate molecule, and compare this with the corresponding value for a single arginine molecule. These findings enable us to predict the conditions under which ligand displacement of surface-adsorbed citrate by arginine may take place. Our findings represent the first steps toward elucidating a more elaborate, detailed atomistic-scale model relating to the biofunctionalization of citrate-capped AuNPs.

Equilibrium conformational ensemble of the intrinsically disordered peptide n16N: linking subdomain structures and function in nacre

n16 is a framework protein family associated with biogenic mineral stabilization, thought to operate at three key interfaces in nacre: protein/β-chitin, protein/protein, and protein/CaCO3. The N-terminal half of this protein, n16N, is known to be active in conferring this mineral stabilization and organization. While some details relating to the stabilization and organization of the mineral are known, the molecular mechanisms that underpin these processes are not yet established. To provide these molecular-scale details, here we explore current hypotheses regarding the possible subdomain organization of n16N, as related to these three interfaces in nacre, by combining outcomes of Replica Exchange with Solute Tempering molecular dynamics simulations with NMR experiments, to investigate the conformational ensemble of n16N in solution. We verify that n16N lacks a well-defined secondary structure, both with and without the presence of Ca(2+) ions, as identified from previous experiments. Our data support the presence of three different, functional subdomains within n16N. Our results reveal that tyrosine, chiefly located in the center of the peptide, plays a multifunctional role in stabilizing conformations of n16N, for intrapeptide and possibly interpeptide interactions. Complementary NMR spectroscopy data confirm the participation of tyrosine in this stabilization. The C-terminal half of n16N, lacking in tyrosine and highly charged, shows substantive conformational diversity and is proposed as a likely site for nucleation of calcium carbonate. Finally, dominant structures from our predicted conformational ensemble suggest the presentation of key residues thought to be critical to the selective binding to β-chitin surfaces.

Structure of arginine overlayers at the aqueous gold interface: implications for nanoparticle assembly.

Adsorption of small biomolecules onto the surface of nanoparticles offers a novel route to generation of nanoparticle assemblies with predictable architectures. Previously, ligand-exchange experiments on citrate-capped gold nanoparticles with the amino acid arginine were reported to support linear nanoparticle assemblies. Here, we use a combination of atomistic modeling with experimental characterization to explore aspects of the assembly hypothesis for these systems. Using molecular simulation, we probe the structural and energetic characteristics of arginine overlayers on the Au(111) surface under aqueous conditions at both low- and high-coverage regimes. In the low-density regime, the arginines lie flat on the surface. At constant composition, these overlayers are found to be lower in energy than the densely packed films, although the latter case appears kinetically stable when arginine is adsorbed via the zwitterion group, exposing the charged guanidinium group to the solvent. Our findings suggest that zwitterion-zwitterion hydrogen bonding at the gold surface and minimization of the electrostatic repulsion between adjacent guanidinium groups play key roles in determining arginine overlayer stability at the aqueous gold interface. Ligand-exchange experiments of citrate-capped gold nanoparticles with arginine derivatives agmatine and N-methyl-l-arginine reveal that modification at the guanidinium group significantly diminishes the propensity for linear assembly of the nanoparticles.

Tristearin bilayers: structure of the aqueous interface and stability in the presence of surfactants

We report results of atomistic molecular dynamics simulations of an industrially-relevant, exemplar triacylglycerol (TAG), namely tristearin (TS), under aqueous conditions, at different temperatures and in the presence of an anionic surfactant, sodium dodecylbenzene sulphonate (SDBS). We predict the TS bilayers to be stable and in a gel phase at temperatures of 350 K and below. At 370 K the lipid bilayer was able to melt, but does not feature a stable liquid-crystalline phase bilayer at this elevated temperature. We also predict the structural characteristics of TS bilayers in the presence of SDBS molecules under aqueous conditions, where surfactant molecules are found to spontaneously insert into the TS bilayers. We model TS bilayers containing different amounts of SDBS, with the presence of SDBS imparting only a moderate effect on the structure of the system. Our study represents the first step in applying atomistic molecular dynamics simulations to the investigation of TAG-aqueous interfaces. Our results suggest that the CHARMM36 force-field appears suitable for the simulation of such systems, although the phase behaviour of the system may be shifted to lower temperatures than is the case for the actual system. Our findings provide a foundation for further simulation studies of the TS-aqueous interface.

Insights into the transport of alkali metal ions doped into a plastic crystal electrolyte

The application of organic ionic plastic crystals (OIPCs) as a new class of solid electrolyte for energy storage devices such as lithium batteries and, more recently, sodium batteries is attracting increasing attention. Key to this is achieving sufficient target ion transport through the material. This requires fundamental understanding of the structure and dynamics of OIPCs that have been doped with the necessary lithium or sodium salts. Here we report, for the first time, the atomic level structure and transport of both lithium and sodium ions in the plastic crystalline phases of an OIPC diethyl(methyl)(isobutyl)phosphonium hexafluorophosphate. These molecular dynamics simulations reveal two types of coordination geometries of the alkali metal ion first solvation shells, which cooperate closely with the metal ion hopping motion. The significantly different ion migration rates between two metal ion doped systems could also be related to the differences in solvation structures.

Testing the transferability of a coarse-grained model to intrinsically disordered proteins

The intermediate-resolution coarse-grained protein model PLUM [T. Bereau and M. Deserno, J. Chem. Phys., 2009, 130, 235106] is used to simulate small systems of intrinsically disordered proteins involved in biomineralisation. With minor adjustments to reduce bias toward stable secondary structure, the model generates conformational ensembles conforming to structural predictions from atomistic simulation. Without additional structural information as input, the model distinguishes regions of the chain by predicted degree of disorder, manifestation of structure, and involvement in chain dimerisation. The model is also able to distinguish dimerisation behaviour between one intrinsically disordered peptide and a closely related mutant. We contrast this against the poor ability of PLUM to model the S1 quartz-binding peptide.

Novel Na+ Ion diffusion mechanism in mixed organic-inorganic ionic liquid electrolyte leading to high Na+ transference number and stable, high rate electrochemical cycling of sodium cells

Ambient temperature sodium batteries hold the promise of a new generation of high energy density, low-cost energy storage technologies. Particularly challenging in sodium electrochemistry is achieving high stability at high charge/discharge rates. We report here mixtures of inorganic/organic cation fluorosulfonamide (FSI) ionic liquids that exhibit unexpectedly high Na+ transference numbers due to a structural diffusion mechanism not previously observed in this type of electrolyte. The electrolyte can therefore support high current density cycling of sodium. We investigate the effect of NaFSI salt concentration in methylpropylpyrrolidinium (C3mpyr) FSI ionic liquid (IL) on the reversible plating and dissolution of sodium metal, both on a copper electrode and in a symmetric Na/Na metal cell. NaFSI is highly soluble in the IL allowing the preparation of mixtures that contain very high Na contents, greater than 3.2 mol/kg (50 mol %) at room temperature. Despite the fact that overall ion diffusivity decreases substantially with increasing alkali salt concentration, we have found that these high Na+ content electrolytes can support higher current densities (1 mA/cm2) and greater stability upon continued cycling. EIS measurements indicate that the interfacial impedance is decreased in the high concentration systems, which provides for a particularly low-resistance solid-electrolyte interphase (SEI), resulting in faster charge transfer at the interface. Na+ transference numbers determined by the Bruce-Vincent method increased substantially with increasing NaFSI content, approaching >0.3 at the saturation concentration limit which may explain the improved performance. NMR spectroscopy, PFG diffusion measurements, and molecular dynamics simulations reveal a changeover to a facile structural diffusion mechanism for sodium ion transport at high concentrations in these electrolytes.