Molecular-scale Structure Research Articles

Structure and reactivity of environmental interfaces: Application of grazing angle X-ray spectroscopy and long-period X-ray standing waves

Chemical processes occurring at environmental interfaces (e.g. mineral–fluid, mineral–organic matter and mineral–biofilm interfaces) have a profound impact on the environmental fate and bioavailability of aqueous metals and other contaminant species. However, the direct analysis of molecular scale structure and properties of environmental interfaces, particularly under “high-pressure” or “wet” conditions is highly challenging. Synchrotron based X-ray scattering and spectroscopic approaches offer numerous advantages, such as the high penetrating power and molecular scale information inherent to X-ray techniques. Yet, the ability to localize information content to environmental interfaces requires challenging experimental configurations. Here, the application of grazing angle X-ray fluorescence techniques is reviewed, including the presentation of a model formalism that allows for quantitative analysis of fluorescent yield profiles and discussion of the experimental setup. Illustrative examples are discussed, particularly in the context of combining results of GI measurements with the results of other complementary interface probes such as crystal truncation rod diffraction and X-ray microprobe spectroscopic studies.

Trace Metal Retention on Biogenic Manganese Oxide Nanoparticles

Manganese oxides produced by microorganisms are abundant environmental nanoparticles whose high retention capacity for toxic trace metals, especially lead, is well established. Until very recently, our knowledge of the molecular-scale structure and reactivity of these biogenic Mn4+ oxide minerals was inferred from studies of synthetic analogues prepared in the laboratory. However, biogenic Mn oxides and their reactions with trace metals now can be investigated directly using X-ray absorption spectroscopy, thus bringing new insights into the molecular mechanisms behind the very high scavenging efficiency of these minerals. This new knowledge has important implications for the remediation of trace metal contamination.

Structure of Mercaptobiphenyl Monolayers on Mercury

The molecular-scale structure and phase behavior of single-component Langmuir films of 4'-methyl-4-mercaptobiphenyl (MMB) and 4'-perfluoromethyl-4-mercaptobiphenyl (FMMB) on mercury were studied using surface tensiometry, grazing incidence X-ray diffraction, and X-ray reflectivity. At low coverages, a condensed but in-plane disordered single layer of surface-parallel molecules is found for both compounds. At high coverages, both compounds exhibit in-plane-ordered phases of standing-up molecules. For MMB, the biphenyl core dominates the structure, yielding a centered-rectangular unit cell with an area A(x) of 21.8 A(2)/molecule, with molecules tilted by approximately 14 degrees from the surface normal in the nearest-neighbor direction, and a coherence length xi of >1000 A for the crystalline domains. For FMMB, the perfluoromethyl group dominates the structure, yielding a hexagonal unit cell with untilted molecules, an area A(x) of 24.2 A(2)/molecule, and a much smaller xi of approximately 110 A. The structure is discussed in comparison with self-assembled monolayers of MMB on crystalline Au(111) and similar-length alkanethiolate SAMs on Au(111) and on mercury. The differences in the structure are discussed and traced to the differences in the substrate's surface structure, and in the molecular cross section and rigidity.

Molecular dynamics study of thermal phenomena in an ultrathin liquid film sheared between solid surfaces: The influence of the crystal plane on energy and momentum transfer at solid-liquid interfaces

A molecular dynamics study has been performed on a liquid film sheared between moving solid walls. Thermal phenomena that occur in the Couette-like flow were examined, including energy conversion from macroscopic flow energy to thermal energy, i.e., viscous heating in the macroscopic sense, and heat conduction from the liquid film to the solid wall via liquid-solid interfaces. Four types of crystal planes of fcc lattice were assumed for the surface of the solid wall. The jumps in velocity and temperature at the interface resulting from deteriorated transfer characteristics of thermal energy and momentum at the interface were observed. It was found that the transfer characteristics of thermal energy and momentum at the interfaces are greatly influenced by the types of crystal plane of the solid wall surface which contacts the liquid film. The mechanism by which such a molecular scale structure influences the energy transfer at the interface was examined by analyzing the molecular motion and its contribution to energy transfer at the solid-liquid interface.

Dissolutive wetting of Ag on Cu: A molecular dynamics simulation study

Reactive wetting in the eutectic AgCu system is studied with molecular dynamics simulations. As Ag(l) spreads on the Cu surface, Cu dissolves into the liquid. The results for reactive wetting are compared to simulations in which no mixing is permitted, demonstrating that wetting kinetics are enhanced by dissolution reactions. The time dependent radius of the droplet R( t) is used to quantify kinetics for the wetting geometry of an infinitely long cylinder spreading on a substrate. Data show that, when dissolution is dominant, spreading is well described by R( t) ∼ ( R 0 t) 1/2, where R 0 is the starting cylinder radius. Contact angle θ( t) data were calculated via a method that accounts for structure near the contact region and compared to data obtained using circular fits to the droplet profile. Significant differences were observed due to molecular scale structure that rapidly evolves near the contact line. This structure exhibits markedly lower θ than what is predicted from droplet profile data and it is proposed to exist throughout most stages of dissolutive wetting. Simulations of AgCu binary liquids spreading on Cu demonstrate that wetting kinetics decrease with increasing Cu in the liquid, further emphasizing that wetting kinetics are intrinsically linked to dissolution kinetics. After dissolution is complete, a Ag-rich monolayer of atoms advances diffusively across the Cu surface.

Complementary characterization by fluorescence and AFM of polyaminosiloxane glass fibers coatings

AR-Glass fibers were coated with the coupling agent 3-aminopropyltriethoxysilane. The polyaminosiloxane coating obtained was characterized: (i) at a molecular scale by using the fluorescence response of pyrene moiety chemically attached (PSA) to the polymer coating and (ii) at a nanoscopic scale by using Atomic Force Microscopy (AFM). After modifying the polymer structure of the coating by the action of different solvents, the data obtained from both techniques were jointly discussed. It was confirmed by AFM that the deposition of the coupling agent on the fibers is in the form of homogeneously distributed ‘islands’. Furthermore, differences in the size of the silane islands were observed when the silanized fibers are subjected to the effect of different solvents. The fluorescence emission from PSA showed that the solvents exert an important structural change in the polyaminosiloxane coating. The correlation between information at a nanoscopic scale (morphology) and at molecular scale (structure) suggested that certain solvents under a subsequent specific evaporation rate rearrange the polymer chains of the glass fibers coating. This rearrangement seems to be a kind of solvophobic effect whose degree depends on the quality of the solvent and the evaporation rate.

Driven Cavity Flow: From Molecular Dynamics to Continuum Hydrodynamics

Molecular dynamics (MD) simulations have been carried out to investigate the slip of fluid in the lid driven cavity flow where the no-slip boundary condition causes unphysical stress divergence. The MD results not only show the existence of fluid slip but also verify the validity of the Navier slip boundary condition. To better understand the fluid slip in this problem, a continuum hydrodynamic model has been formulated based upon the MD verification of the Navier boundary condition (NBC) and the Newtonian stress. Our model has no adjustable parameter because all the material parameters (density, viscosity, and slip length) are directly determined from MD simulations. Steady-state velocity fields from continuum calculations are in quantitative agreement with those from MD simulations, from the molecular-scale structure to the global flow. The main discovery is as follows. In the immediate vicinity of the corners where moving and fixed solid surfaces intersect, there is a core partial-slip region where the...

Solid–Liquid Interfaces: Molecular Structure, Thermodynamics, and Crystallization

AbstractMaterials phenomena ranging from the melting or freezing of ice to biomineralization in living organisms, to lubrication and the commercial casting of superalloys, are known to be critically influenced by molecular-scale structure and processes occurring at the interfaces between the crystalline solid and liquid phases. The properties of solid–liquid interfaces have long been a topic of intense interest in materials science, primarily because of their role in governing nucleation, growth, and morphological evolution in crystal growth from the melt or solutions.This issue of the MRS Bulletin provides an overview, highlighting new developments in experiment, theory, and modeling techniques that have led to substantial recent progress in the characterization of the molecular-level structural and thermodynamic properties of solid–liquid interfaces and their consequences for a variety of crystallization phenomena.

Molecular scale structure formation by folding

A conception of a structure formation suitable for nano-technology is proposed, which is programmable and suitable for mass production-like lithography. This conception utilizes the controlled folding of chains like the scan-lines of television. Its possibility and property were studied theoretically using the modeled chains consist of beads. By adopting the interaction among the beads which can distinguish the kind of the partner by its polarity and is chiral to break the chiral symmetry of the folded state, the special chains which have the unique ground states could be designed. In these ground states, the chains are folded like the scan-lines of television. The thermodynamic properties of the suggested chains were studied by the Monte Carlo simulations and the suggested chains showed the phase-transition-like behavior which is distinct compared to both the random chains and the chain that has only the non-specific attraction. The size dependence and the effects of adding the non-specific attraction and modifying the border of the folded conformation were also studied.

NEW INSIGHT INTO MICROSCALE TRANSPORT PHENOMENA IN PEFC BY QUANTUM MD

Polymer electrolyte fuel cells (PEFCs) are among the most promising energy equipment options because of its high power density and efficiency; however, there are numerous technical problems to commercialize this technique, and understanding the critical phenomena for the performance of PEFC is essential. We performed the molecular simulation study about oxygen reduction reaction on the cathode catalyst and mass transport in the polymer electrolyte. We performed two kinds of simulations based on the first principle's molecular dynamics to elucidate oxygen reduction reaction, the finite temperature simulation of oxygen reduction reaction on the clean platinum surface, and the energy minimization simulation of oxygen adsorption on the various transition metals. We acquired novel information concerning the mechanism of oxygen reduction reaction, and it was found that one of the most critical factors for the catalysis was the oxygen adsorption structure on the clean platinum surface. We also employed the molecular dynamics study of mass transport in the polymer electrolyte. It successfully reproduced the experimental results. Moreover, we acquired information about the molecular scale structure and the transport mechanism in the polymer electrolyte. We proposed guiding principles for designing high conductive electrolytes based on these results.

Molecular segregation observed in a concentrated alcohol-water solution.

When a simple alcohol such as methanol or ethanol is mixed with water, the entropy of the system increases far less than expected for an ideal solution of randomly mixed molecules. This well-known effect has been attributed to hydrophobic headgroups creating ice-like or clathrate-like structures in the surrounding water, although experimental support for this hypothesis is scarce. In fact, an increasing amount of experimental and theoretical work suggests that the hydrophobic headgroups of alcohol molecules in aqueous solution cluster together. However, a consistent description of the details of this self-association is lacking. Here we use neutron diffraction with isotope substitution to probe the molecular-scale structure of a concentrated alcohol water mixture (7:3 molar ratio). Our data indicate that most of the water molecules exist as small hydrogen-bonded strings and clusters in a 'fluid' of close-packed methyl groups, with water clusters bridging neighbouring methanol hydroxyl groups through hydrogen bonding. This behaviour suggests that the anomalous thermodynamics of water alcohol systems arises from incomplete mixing at the molecular level and from retention of remnants of the three-dimensional hydrogen-bonded network structure of bulk water.

Microscopic structure and dynamics of a partial bilayer smectic liquid crystal.

Cyanobiphenyls (nCB's) represent a useful and intensively studied class of mesogens. Many of the peculiar properties of nCB's (e.g., the occurrence of the partial bilayer smectic-A(d) phase) are thought to be a manifestation of short-range antiparallel association of neighboring molecules, resulting from strong dipole-dipole interactions between cyano groups. To test and extend existing models of microscopic ordering in nCB's, we carry out large-scale atomistic simulation studies of the microscopic structure and dynamics of the Sm-A(d) phase of 4-octyl-4'-cyanobiphenyl (8CB). We compute a variety of thermodynamic, structural, and dynamical properties for this material, and make a detailed comparison of our results with experimental measurements in order to validate our molecular model. Semiquantitative agreement with experiment is found: the smectic layer spacing and mass density are well reproduced, translational diffusion constants are similar to experiment, but the orientational ordering of alkyl chains is overestimated. This simulation provides a detailed picture of molecular conformation, smectic layer structure, and intermolecular correlations in Sm-A(d) 8CB, and demonstrates that pronounced short-range antiparallel association of molecules arising from dipole-dipole interactions plays a dominant role in determining the molecular-scale structure of 8CB.

Diffusion of paramagnetically labeled proteins in cartilage: enhancement of the 1-D NMR imaging technique.

Quantifying the diffusive transport of large molecules in avascular cartilage tissue is important both for planning potential pharamacological treatments and for gaining insight into the molecular-scale structure of cartilage. In this work, the diffusion coefficients of gadolinium-DTPA and Gd-labeled versions of four proteins-lysozyme, trypsinogen, ovalbumin, and bovine serum albumin (BSA) with molecular weights of 14,300, 24,000, 45,000, and 67,000, respectively-have been measured in healthy and degraded calf cartilage. The experimental technique relies on the effect of the paramagnetic on the relaxation properties of the surrounding water, combined with the time course of a 1-dimensional spatial profile of the water signal in the cartilage sample. The enhanced technique presented here does not require a prior measurement of the relaxivity of the paramagnetic compound in the sample of interest. The data are expressed as the ratio of the diffusion coefficient of a compound in cartilage to its diffusion coefficient in water. For healthy cartilage, this ratio was 0.34 +/- 0.07 for Gd-DTPA, the smallest compound, and fell to 0.3 +/- 0.1 for Gd-lysozyme, 0.08 +/- 0.04 for Gd-trypsinogen, and 0.07 +/- 0.04 for Gd-ovalbumin. Gd-BSA did not appear to enter healthy cartilage tissue beyond a surface layer. After the cartilage had been degraded by 24-h trypsinization, these ratios were 0.60 +/- 0.03 for Gd-DTPA, 0.40 +/- 0.08 for Gd-lysozyme, 0.42 +/- 0.09 for Gd-trypsinogen, 0.16 +/- 0.14 for Gd-ovalbumin, and 0.11 +/- 0.05 for Gd-BSA. Thus, degradation of the cartilage led to increases in the diffusion coefficient of up to fivefold for the Gd-labeled proteins. These basic transport parameters yield insights on the nature of pore sizes and chemical-matrix interactions in the cartilage tissue and may prove diagnostically useful for identifying the degree and nature of damage to cartilage.

Molecular structure and orientation in processed polymers: 1. Analysis of X-ray scattering data

We present a method for analyzing the molecular scale orientation and structure of processed polymers using wide angle X-ray scattering data (WAXS). The technique is applied to the analysis of solution-spun fibers of a liquid crystalline polyester comprised of 1,4-hydroxybenzoic acid, isophthalic acid, and hydroquinone. The orientation distribution function (ODF) of the non-crystalline component of the polyester is constructed using a Legendre polynomial series expansion. To construct a consistent molecular scale description, a Monte Carlo sampling scheme which incorporates the standard Metropolis sampling was employed, coupled with a weighting factor that favors structures which are in closer accord with the experimental WAXS data. The members of the ensemble sampled by the simulation consist of rhombic lattices on which oligomers are placed in an aligned state. The conformation of each oligomer was obtained using a rotational isomeric state description. By direct comparison of the experimental and calculated structure factor coefficients, the ODF for the structural ensemble was deduced. For the polyester fiber considered here, a two-component system consisting of oriented and unoriented non-crystalline components is required for complete characterization of the scattering properties of the sample. The sample contains a negligible amount of crystalline material, but 85% of the sample is aligned locally (i.e. with respect to nearest neighbor chains). However, as the fibers are spun from an isotropic solution, the global orientation (i.e. orientation with respect to the sample axis) remains low.

Molecular structure and orientation in processed polymers: 2. Application to aromatic polyester fibers

We characterize the orientation distribution function (ODF) of molecular-scale structure in a set of solution- and melt-spun fibers of a liquid crystalline polyester in order to assess the role of processing in these fibers. The polyester is composed of 40% 1,4-hydroxybenzoic acid, 30% isophthalic acid, and 30% hydroquinone. Crystallinity is measured by both wide angle X-ray scattering (WAXS) and differential scanning calorimetry (DSC). A three-component model, consisting of crystalline, oriented non-crystalline, and unoriented non-crystalline components, is required to describe completely the X-ray scattering properties of the fibers. Monte Carlo simulations are used to define the ensemble structure on the atomic scale, for which the resulting ODF is determined. Our results indicate that a single ensemble of dimers on a 3×3 rhombic lattice can be used to characterize the molecular-level non-crystalline structure in all the fibers considered. Fibers spun from the nematic melt produce samples with higher degrees of global orientation as well as a higher degree of crystallinity than those spun from solution. Our results also show that the mechanical bias of the fiber spinning process induces an initial degree of orientation which is then enhanced and perfected, especially in the directions lateral to the chain, by subsequent annealing.

The role of microstructure in taming the Rayleigh capillary instability of cylindrical jets

It is observed both in nature and in technological processes that filaments with anisotropic molecular-scale structure are less susceptible to breakup due to capillary instability than homogeneous, isotropic fluids in similar filament flows. Here we provide rigorous evidence that the strong coupling of microstructure to the hydrodynamics of cylindrical axisymmetric free surface filaments, indeed fundamentally alters the linearized stability of cylindrical jets. We extend Rayleigh's classical inviscid analysis of cylindrical jets to the three-dimensional (3D), macroscopic flow-orientation equations derived from the Doi kinetic theory for liquid crystalline polymers (LCPs). These equations assume rigid rod-like molecules and incorporate LCP effects of molecular relaxation, anisotropic drag, polymer kinetic energy, LCP density, and an intermolecular potential which couple orientation dynamics to standard free surface fluid equations. Depending on the LCP density, there are between one and three flow-independent orientation equilibria which persist in a constant-velocity, cylindrical free surface flow: an isotropic phase exists at all concentrations, whereas two anisotropic phases exist at sufficiently high LCP density. These equilibrium LCP cylindrical jets have two independent sources of instability, hydrodynamic and orientational, each identified within the coupled flow/orientation free surface equations. For this paper we restrict to equilibria free of orientational instabilities. All streamwise perturbations of wavelength greater than the jet circumference are unstable to capillary instability; only the strength of the instability and most dominant wavelength are affected by LCP microstructure. The degree to which microstructure reduces the capillary instability depends on two critical scaling parameters: an LCP capillary number Ca lcp (a ratio of LCP-induced surface stress to interfacial capillary stress); and the anisotropic drag/friction parameter σ. The most striking result is: for sufficiently large Ca lcp and highly anisotropic drag ( σ ∼ 0) the capillary growthrate can be uniformly lowered, arbitrarily close to zero. For sufficiently small Ca lcp, all capillary-dominated growthrates are reduced, but are bounded below in terms of an explicit, sharp estimate and bounded above by the Rayleigh formula. The upshot is: inviscid LCP jets are predicted to yield bigger drops which form on longer timescales than an inviscid isotropic fluid with the same surface tension.

Peer Reviewed: Applications of Fluorescence Recovery after Photobleaching

Determining the diffusion coefficients of fluorescent molecules provides details on molecular-scale structure.

Monte Carlo simulations of racemic liquid mixtures: thermodynamic properties and local structure

NPT Monte Carlo simulations of racemic mixtures were performed on a simplified model for the enantiomers. The molecules were spheres of equal size, interacting via a modified LennardJones potential. The interaction strength and the optimum distance between heterochiral molecules (D and L) differed (by a factor e and a factor s, respectively) from the homochiral values (D and D or L and L). Chemical potentials, enthalpies and orientational bond order parameters Q l were calculated for a lot of racemic liquid mixtures. Weak heterochiral interactions (e < 1) showed a tendency to phase separation. Extremely strong interactions (e ≈ 5) gave rise to a glassy phase. A correlation analysis of the measured Q l values for e ≠ / 1 and s = 1 showed no similarity of the molecular scale structure with that of binary crystals. Mixtures with s < 1 and with s > 1 both had a negative excess entropy, showing ordering. This effect was outweighed by a large negative excess enthalpy, and in total they had a negative excess Gibbs energy. In these mixtures the molecular scale structure was similar to that of certain binary crystal structures. By comparing the measured Q l values with those for ideal reference crystals an NaCl-like ordering was found for small s and various layered closepacked crystal structures for larger s.

Structural Developments in Fragile Glass Forming Oxides

ABSTRACTBrillouin light has been used to measure the complex mechanical modulus of the molecular scale structure in oxide melts. The storage modulus reflects the degree of networking and structural integrity, while the loss modulus, which can be attributed to aperiodic motions of structural components, provides a measure of the mobility of these entities. rom the loss modulus it is possible to derive the zero-shear rate viscosity, which is characteristic of a structure in thermodynamic equilibrium, and thereby provide a less encumbered insight into the molecular scale mechanisms that are underlying to the viscous momentum transport.In this paper we compare the visco-elastic behavior of alkali borates and alkali tellurites, particularly in the temperature range between Tg and the equilibrium melting point. While in borates several mechanisms can be identified as contributing to structural relaxation, in tellurites a single mechanism dominates. The assumption of thermo-rheological simplicity, however, is invalid, and a new visco-elastic model has been developed for the description of our results.

Scanning tunneling microscopy of unbroken chloroplasts

Mainsbridge and Thundat [J. Vac. Sci. Technol. B 9 (1991) 1259] recently reported STM images of chloroplast components. The goal of our work was to investigate the effects of sample preparation and imaging conditions, and to more clearly identify some of the structures that appear in chloroplast images. We have imaged gold-coated chloroplasts in air, and bare chloroplasts in solution. Results obtained include images of whole chloroplasts several micrometers in diameter, and images which show molecular-scale structure on the chloroplast outer membrane.