Partial Structure Factors Research Articles

The structure of manganese dioxide and position of proton studied by neutron diffraction with isotopic substitution

The position of proton inside manganese dioxide, γ-MnO 2, was studied by the total neutron-scattering technique using H/D isotopic substitution. The first-order difference was obtained by subtracting the results for the two different isotopic compositions and obtaining the weighted sum of partial structure factors and radial distribution functions related to the structure around hydrogens. The deuterium-substituted γ-MnO 2 was prepared by de-intercalation of the proton via an oxidative treatment prior to re-intercalation with deuterium. The proton occupied two different positions with the H–O length of 1.0 and 1.9 Å, which corresponds to the ‘Ruetschi’ and ‘Coleman’ protons, respectively. The former protons situated in the Mn 4+ vacant site and the latter in the tunnel centered in an oxygen octahedron. The isotopic substitution technique and the structure around protons are discussed in details.

Interionic pair potentials and partial structure factors of compound-forming quaternary NaSn liquid alloy: First principle approach

In this paper formulae for partial structure factors have been used to study partial structure factors of compound-forming quaternary liquid alloys by considering Hoshino’s m-component hard-sphere mixture, which is based on Percus-Yevic equation of Hiroike. Formulae are applied to NaSn (Na, Sn, NaSn, Na3Sn) which is considered as a quaternary liquid mixture with the formation of two compounds simultaneously. We have compared the total structure factors for ternary and quaternary alloys with experimental total structure factors which are found to be in good agreement. This suggests that, for suitable stoichiometric composition, two compounds are formed simultaneously. The hard-sphere diameters needed have been calculated using Troullier and Martins ab-initio pseudopotentials.

Structural properties of amorphousGeSe2

By using first-principles molecular dynamics within densityfunctional theory, we study the structural properties of amorphousGeSe2 atT = 300 K. The amorphous configurations have been obtained via coolingfrom the liquid state followed by extensive relaxation (22 ps) atT = 300 K. The agreement with neutron diffraction experiments is very satisfactory, inparticular for the pair correlation functions in real space and the partial structurefactors in reciprocal space describing the Ge–Se and the Se–Se correlations.Some residual differences between theory and experiment are found for Ge–Gecorrelations. The network organizes itself through the predominant presence ofGeSe4 tetrahedra. However, other coordinations exist in non-negligible proportions for both Geand Se. Homopolar bonds are found for Se, and, in a very limited extent, also forGe. The number of edge-sharing connections reproduces the experimental data.

Structure of glassy GeO2

The full set of partial structure factors for glassy germania, orGeO2, were accurately measured by using the method of isotopic substitution inneutron diffraction in order to elucidate the nature of the pair correlations forthis archetypal strong glass former. The results show that the basic tetrahedralGe(O1/2)4 building blocks share corners with a mean inter-tetrahedral Ge–Ô–Ge bond angle of132(2)°. The topological and chemical ordering in the resultant network displays two characteristiclength scales at distances greater than the nearest neighbour. One of these describesthe intermediate range order, and manifests itself by the appearance of a firstsharp diffraction peak in the measured diffraction patterns at a scattering vectorkFSDP≈1.53 Å−1,while the other describes so-called extended range order, and is associated with the principal peakat kPP = 2.66(1) Å−1. We find that there is an interplay between the relative importance of the ordering on theselength scales for tetrahedral network forming glasses that is dominated by the extended rangeordering with increasing glass fragility. The measured partial structure factors for glassyGeO2 are used to reproduce the total structure factor measured by using high energy x-raydiffraction and the experimental results are also compared to those obtained by usingclassical and first principles molecular dynamics simulations.

Effects of surface pressure on the structure of the monolayer formed at the air/water interface by a non-ionic surfactant

The monolayer formed at an air/water interface by the synthetic non-ionic surfactant, 1,2-di- O-octadecyl- rac-glyceryl-3-( ω-methoxydodecakis (ethylene glycol)) (2C 18E 12) has been characterized using Langmuir trough measurements, Brewster angle microscopy (BAM), and neutron reflectometry. The BAM and reflectometry studies were performed at four different surface pressures ( π) in the range 15–40 mN/m. The BAM studies (which give information on the in-plane organisation of the surfactant layer) demonstrate that the 2C 18E 12 molecules are arranged on the water surface to form distinct, approximately circular, 5 μm diameter domains. As the surface pressure is increased these domains retain their size and shape but are made progressively more close-packed, such that the monolayer is made more or less complete at π = 40 mN / m . The neutron reflectometry measurements were made to determine the structure of the interfacial surfactant layer at π = 15 , 28, 34 and 40 mN/m, providing information on the thickness of the 2C 18E 12 alkyl chains', head groups' and associated solvent distributions (measured along the surface normal), along with the separations between these distributions, and the effective interfacial area per molecule. Partial structure factor analyses of the reflectivity data show that the effective interfacial area occupied decreases from 217 Å 2 per 2C 18E 12 molecule at π = 15 mN / m down to 102 Å 2 at π = 40 mN / m . There are concomitant increases in the widths of the surfactant's alkyl chains' and head groups' distributions (modelled as Gaussians), with the former rising from 12 Å (at π = 15 mN / m ) up to 19 Å (at π = 40 mN / m ) and the latter rising from 13 Å (at π = 15 mN / m ) up to 24 Å (at π = 40 mN / m ). The compression of the monolayer is also shown to give rise to an increased surface roughness, some of which is due to the thermal roughness caused by capillary waves, but with a significant contribution also coming from the intrinsic/structural disorder in the monolayer. At all surface pressures studied, the alkyl chains and head groups of the 2C 18E 12 are found to exhibit a significant overlap, and this increases with increasing π. Given the various trends noted on how the structure of the 2C 18E 12 monolayer changes as a function of π, we extrapolate to consider the structure of the monolayer at π > 40 mN / m (making comparison with its single chain (C n E m ) counterparts) and then relate these findings to the observations recorded on the structure and solute entrapment efficiency of 2C 18E 12 vesicles.

Collective and static properties of model two-component plasmas

Classical MD data on the charge-charge dynamic structure factor of two-component plasmas (TCP) modeled in Phys. Rev. A 23, 2041 (1981) are analyzed using the sum rules and other exact relations. The convergent power moments of the imaginary part of the model system dielectric function are expressed in terms of its partial static structure factors, which are computed by the method of hypernetted chains using the Deutsch effective potential. High-frequency asymptotic behavior of the dielectric function is specified to include the effects of inverse bremsstrahlung. The agreement with the MD data is improved, and important statistical characteristics of the model TCP, such as the probability to find both electron and ion at one point, are determined.

Dynamic structure of molten CuI: Ab initio molecular-dynamics simulations

The dynamic properties of molten CuI are studied by ab initio molecular-dynamics simulations. The frequency spectrum of the velocity auto-correlation function for Cu ions spreads over higher frequencies than 20meV, which reflects a peculiar interaction between Cu ions. It is shown that the calculated dynamic structure factors are in good agreement with the recent inelastic X-ray scattering experiments. The narrowing in the partial dynamic structure factors for Cu and I ions is found at the wave number of about 1.0 and 1.8Å−1, respectively.

Normal-Mode Refinement of Anisotropic Thermal Parameters for Potassium Channel KcsA at 3.2 Å Crystallographic Resolution

We report a normal-mode method for anisotropic refinement of membrane-protein structures, based on a hypothesis that the global near-native-state disordering of membrane proteins in crystals follows low-frequency normal modes. Thus, a small set of modes is sufficient to represent the anisotropic thermal motions in X-ray crystallographic refinement. By applying the method to potassium channel KcsA at 3.2 A, we obtained a structural model with an improved fit with the diffraction data. Moreover, the improved electron density maps allowed for large structural adjustments for 12 residues in each subunit, including the rebuilding of 3 missing side chains. Overall, the anisotropic KcsA structure at 3.2 A was systematically closer to a 2.0 A KcsA structure, especially in the selectivity filter. Furthermore, the anisotropic thermal ellipsoids from the refinement revealed functionally relevant structural flexibility. We expect this method to be a valuable tool for structural refinement of many membrane proteins with moderate-resolution diffraction data.

Structure of liquids and glasses in the Ge–Se binary system

A summary is given of the partial structure factors that have been measured for liquids and glasses in the Ge–Se binary system by using diffraction methods. Information is presented on the pair correlation functions describing the atomic species and use is made of the Bhatia–Thornton formalism to separate those pair correlation functions describing the system topology from those that describe the chemical ordering. The information made available by the measured Bhatia–Thornton partial structure factors on the thermodynamic properties of Ge–Se mixtures is briefly summarized. The properties of the network structures formed in liquid and glassy Ge–Se compounds are investigated as a function of composition, temperature and pressure. For GeSe2 at ambient pressure it is shown that the so-called first sharp diffraction peak, which appears in the measured diffraction patterns at a small scattering wavevector value of ≈1Å−1 and which is associated primarily with Ge–Ge correlations, does account for discernable features of the observed intermediate range order in both the liquid and glassy phase. The first sharp diffraction peak in the measured Ge–Ge partial structure factor for both phases is described by comparable parameters suggesting communality in the underlying intermediate range order which survives the glass transition. Homopolar bonds are found to be a feature in the structure of liquid GeSe and both liquid and glassy GeSe2 with Ge–Ge and Se–Se distances in the ranges 2.33(3)–2.42(2) and 2.30(2)–2.34(2)Å, respectively.

PEO−PPO Block Copolymer Vectors Do Not Interact Directly with DNA but with Lipid Membranes

Small angle neutron (SANS) and light scattering was used to study the interaction between fragments of double stranded deoxyribonucleic acid (DNA) and a synthetic triblock [poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide)] amphiphilic polymer, known as L64, a potential vector for gene therapy. The mechanism of action of this vector is yet unknown. The contrast variation method was used to separate the partial structure factors of the different components in mixtures of triblock and DNA. It has been found that the copolymer and DNA molecules exhibit repulsive interactions. Further, the interaction between the copolymer and a model lipid membrane was investigated in order to explain the action of the vector. Electrical measurements on black lipid membranes indicated that the main effect of L64 as a vector is to permeabilize the cell's membrane.

Modeling the structural, dynamical, and magnetic properties of liquidAl1−xMnx(x=0.14, 0.2, and 0.4): A first-principles investigation

We report the results of first-principles molecular dynamics simulations of liquid ${\mathrm{Al}}_{1\ensuremath{-}x}{\mathrm{Mn}}_{x}$ alloys at three different compositions. The local structure as defined by the Bhatia-Thornton partial structure factors is found to display significant changes at $x=0.4$. In addition, a structural analysis using three-dimensional pair-analysis techniques evidences a fivefold symmetry around $x=0.14$, in agreement with the experimental quasicrystal-forming range, and an increasing complexity of the Frank-Kasper polytetrahedral symmetry around Mn atoms at $x=0.4$. We also examine the time evolution of the configurations at the three compositions in terms of the mean-square displacements and self-diffusion coefficients. Finally, we show a strong interplay between the structural changes and the evolution of the magnetic properties of the Mn atoms as a function of composition.

Concentration fluctuations in liquid alloys of alkali metals

Large-scale molecular dynamics simulations are performed to study the structure of liquid alloys of alkali metals (namely K–CS, Na–K, and Na–Cs) on the whole range of composition. The interactions are described by Fiolhais’ pseudopotential that has already proven its ability to describe the interactions in pure liquid alkali metals. By a comparison of the total structure factor with experimental results, the transferability of the description of the interactions is ascertained for all these systems on the whole composition range. Since these systems exhibit different behaviors at the level of the composition fluctuations, partial pair distribution functions and Bathia–Thornton’s partial structure factors are displayed for some representative compositions. The influence of the characteristics of the interactions on these fluctuations is examined. Size mismatch as well as energetic non-additivity favor heterocoordination while the attraction asymmetry encourages homocoordination. A competition between these two effects is pointed out.

Experimental ordering potential of manganese-polyvalent metals

Manganese is one of the scarce metals which presents a negative scattering length. It is thus possible, by measuring the total structure factor at a given concentration corresponding to that of the ‘zero alloy’, to obtain experimentally the Bhatia–Thornton concentration–concentration partial structure factor SCC(q), from which the ordering potential can be obtained. We present three experimental ordering potentials of Mn60Sb40 (950°C), Mn69Ge31 (980°C) and Mn66Ga34 (1050°C), which govern the order in the binary alloys. The comparison between these three potentials reveals interesting features especially when their depth and shape is analysed in relation with the electronegativity and the size differences of the considered atoms.

Experimental and RMC simulation study of liquid Cu6Sn5

The atomic structure of liquid Cu6Sn5 alloy at 640°C has been investigated with neutron and X-ray diffraction. The experimental structure factors were used to perform computer modeling with the reverse Monte Carlo method. Three different series of simulations were carried out. It has been established that the partial structure factors modeled by combining the experimental data of the two independent measurements (XRD and ND) are reliable, while those modeled with only one set of the experimental data (XRD or ND) exhibit some non-physical features.

Structural Analysis of Polyelectrolyte Film Absorbing Metal Ion by SAXS Utilizing with X-ray Anomalous Dispersion Effect

A distribution of Cu ions in polyelectrolyte film (Nafion) is directly observed with a small-angle X-ray scattering (SAXS) method utilizing an X-ray anomalous dispersion effect. A partial structure factor of the Cu ions, GAA(q), can be derived from the SAXS profiles obtained by scanning the incident X-ray energy around the Cu K absorption edge. GAA(q) has two peaks, indicating that the Cu ions hierarchically distribute in Nafion film. In addition, a standard SAXS also shows that Nafion film has a hierarchical structure. These results mean that the Cu ions locate in the domain where the hydrophilic bases aggregate.

First-principles investigation of the structural and vibrational properties of vitreousGeSe2

Using a density-functional scheme, we study the structural and vibrational properties of vitreous germanium diselenide $(v\text{\ensuremath{-}}\mathrm{Ge}{\mathrm{Se}}_{2})$. Through the use of classical and first-principles molecular-dynamics methods, we generate a set of structural models showing a varying degree of chemical disorder. In particular, two types of structural concepts are represented: one in which the tetrahedral order is preserved to a very large extent, and one which reproduces the high degree of disorder in first-neighbor shells found in first-principles molecular-dynamics simulations of the liquid. The investigated structural properties include the angular distributions, the atomic arrangements in the first-neighbor shells, and the pair-correlation functions. In reciprocal space, we have calculated the x-ray and neutron total structure factors and the partial structure factors. Comparison with experiment gives overall good agreement for the models of either structural conception. We then investigate the vibrational properties via the vibrational density of states and the inelastic neutron spectrum. The considered models yield similar spectra and agree with experimental data. We also obtain infrared and Raman spectra through a density-functional scheme based on the application of finite electric fields. For these spectra, significant differences appear among the models. The comparison with experiment favors a model showing a high degree of chemical order. The Raman intensity is analyzed in terms of the underlying atomic vibrations. The assignment of the Raman companion line to Se motions in edge-sharing tetrahedra is supported.

The structural properties of the liquid CdTe based on Reverse Monte Carlo modelling

The Reverse Monte Carlo (RMC) method only provides information on structure, not on dynamics, and so has restricted applicability. We have only attempted to describe the trends in structural terms. The static structure of liquid Cadmium Telluride is performed using RMC modelling technique fitting to neutron diffraction data. In order to retain its tetrahedral environment with the coordination number about four in its liquid state, we have used some plausible physical constraints. In this way, it is possible to derive static structure of liquid CdTe with analysing the experimental data. We have shown the results for the partial static structure factors S ij ( q) and the partial pair distribution functions g ij ( r). We have also determined the distribution of the number of neighbors within the first coordination shell and calculated the bond angle distribution. A good agreement with the experiment is observed for the structural properties of liquid CdTe.

Structure modeling for covalently bonded network glasses

The structure of covalently bonded network glasses is investigated in detail, through the example of GeSe 2, using a combination of experimental and computational tools. Experimentally, neutron and high-energy X-ray diffraction measurements have been carried out on amorphous GeSe 2 at KENS-KEK and SPring-8, respectively, and are used in conjunction with data from a previous neutron diffraction with isotopic substitution (NDIS) study [Petri et al., Phys. Rev. Lett. 84 (2000) 2413]. Reverse Monte Carlo modeling, employing the GeSe 2 crystal structure as a computational starting point, reproduces well the partial structure factors obtained from NDIS. RMC simulations also model well the total structure factors of the current neutron and X-ray diffraction experimental data. The analysis of all results reinforce evidence for intermediate range ordering in GeSe 2 glasses, and suggest that atomic arrangements of Ge atoms are considered to have a very important role for this intermediate range ordering.

Phasing of resonant anomalous X-ray reflectivity spectra and direct Fourier synthesis of element-specific partial structures at buried interfaces

A formalism for model-independent determination of element-specific partial structures at buried interfaces using the phase-dependent behavior of resonant anomalous X-ray reflectivity (RAXR) data is described. Each RAXR spectrum (i.e.reflectivityversusenergy at a fixed momentum transfer near the absorption edge of interest) is uniquely constrained by the amplitude and phase of the resonant partial structure factor with pre-determined non-resonant total structure factor and anomalous dispersion corrections of the resonant species. The element-specific partial density distribution is then imaged by discrete Fourier synthesis with the partial structure factor. The utility of this approach is demonstrated in the comparison of Rb+and Sr2+distributions at muscovite (001)–aqueous solution interfaces derived by model-independent and model-dependent approaches. This imaging method is useful for rapid determination of complex buried interfacial structures where element-specific atomic distributions are poorly constrained by conventional X-ray reflectivity analysis.

Ionic dynamics of molten cuprous iodide

Quasi-elastic neutron scattering measurements have been performed in order to investigate ionic dynamics in molten CuI at 650 °C. The prominent elastic contribution was observed at around 0.85 Å −1, where the partial structure factor of the Cu–Cu correlation has the first sharp diffraction peak. The analysis of the relaxation time in the intermediate scattering functions deduced from the quasi-elastic scattering spectra reveals that molten CuI exhibits extremely slow dynamics with the characteristic relaxation time over 1 ps in this Q-region, which is much longer than the self-diffusion of Cu ions.