Experimental Intensity Curves Research Articles

Fragmentary Model of the Atomic Structure of the Ion-Conducting Semiconductor Glass AgGeAsSe3

The atomic radial distribution function of vitreous AgGeAsSe3, obtained based on the experimental intensity curves taken with monochromatic copper and molybdenum radiation, is interpreted using a fragmentary model in the entire ordering region (~9 Å). It is shown that the glass consists of selenium and selenium-arsenic tetrahedra with germanium and silver atoms inside. The spatial arrangement of such tetrahedra in glass within the ordering region is similar to their arrangement in the GeAsSe and GeSe2 structures. It is proposed that the “openwork” structure of the fragments of these structures allows the movement of Ag+ ions (ionic conductivity) in vitreous AgGeAsSe3. Fragments of the structure of the ion-conducting compound Ag2Se are not found in the studied glass.

SAXSMoW 2.0: Online calculator of the molecular weight of proteins in dilute solution from experimental SAXS data measured on a relative scale.

Knowledge of molecular weight, oligomeric states, and quaternary arrangements of proteins in solution is fundamental for understanding their molecular functions and activities. We describe here a program SAXSMoW 2.0 for robust and quick determination of molecular weight and oligomeric state of proteins in dilute solution, starting from a single experimental small-angle scattering intensity curve, I(q), measured on a relative scale. The first version of this calculator has been widely used during the last decade and applied to analyze experimental SAXS data of many proteins and protein complexes. SAXSMoW 2.0 exhibits new features which allow for the direct input of experimental intensity curves and also automatic modes for quick determinations of the radius of gyration, volume, and molecular weight. The new program was extensively tested by applying it to many experimental SAXS curves downloaded from the open databases, corresponding to proteins with different shapes and molecular weights ranging from ~10 kDa up to about ~500 kDa and different shapes from globular to elongated. These tests reveal that the use of SAXSMoW 2.0 allows for determinations of molecular weights of proteins in dilute solution with a median discrepancy of about 12% for globular proteins. In case of elongated molecules, discrepancy value can be significantly higher. Our tests show discrepancies of approximately 21% for the proteins with molecular shape aspect ratios up to 18.

STRUCTURE OF NEAREST ENVIRONMENT OF IONS IN AQUEOUS CESIUM IODIDE SOLUTIONS FROM X-RAY DIFFRACTION DATA

Comparatively large amount of works has been devoted to the investigation of the nearest environment of cesium ions in aqueous solutions. But up to date there are no precise quantitative parameters of it. Information about influence of concentration on cesium salts solutions structure is also absent. In order to get the coordination number of Cs+ ion and its dependence on the amount of dissolved salt the set of aqueous solutions of cesium iodide have been studied by X-ray diffraction method in wide concentration range under ambient conditions. Radial distribution functions (RDFs) of the solutions investigated have been calculated from experimental intensity curves of X-ray scattering. Interpretation of experimental peaks on RDFs has been made. On the basis of experimental results and literature information some physically reasonable models of solution have been constructed. Theoretical RDFs have been calculated for every model. Then an optimization procedure has also been made. On the ground of the best fitness between experimental and theoretical RDFs the optimal models for every solution have been found. All quantitative parameters have been tabulated and analyzed. Hydration numbers of Cs+ and I- increase with dilution, reaching in the solution of molar ratio 1:80 values 6.3 and 4.1, respectively. Interparticle distances of Cs+–ОН2 and I- –ОН2 are equal approximately to 0.312 and 0.359 nm. The ions do not form the second coordination shells. It has been determined that contact ion pairs Cs+–I- exist in whole concentration range investigated.Forcitation:Smirnov P.R., Grechin O.V., Voevodina E.A. Structure of nearest environment of ions in aqueous cesium iodide solutions from X-ray diffraction data. Izv. Vyssh. Uchebn. Zaved. Khim. Khim. Tekhnol. 2017. V. 60. N 7. P. 21-26.

MOLECULAR STRUCTURE OF TRIS(ACETYLACETONATE)IRON STUDIED BY GAS-PHASE ELECTRON DIFFRACTION AND DFT CALCULATIONS

The molecular structure of tris(acetylacetonate)iron, Fe(O2C5H7)3, has been determined by synchronous gas-phase electron diffraction and mass spectrometric experiment along with quantum chemical calculations at the DFT/UB3LYP/cc-pVTZ theory level. The best agreement between theoretical and experimental intensity curves of scattered electrons was obtained for the high spin model with the symmetry D3 of molecule. The DFT calculations also resulted in high spin electronic state 6A1 of the molecule Fe(O2C5H7)3 as the ground one at the geometrical configuration of D3 symmetry.Forcitation:Petrova A.A., Tverdova N.V., Giricheva N.I. Girichev G.V. Molecular structure of tris(acetylacetonate)iron studied by gas-phase electron diffraction and DFT calculations. Izv. Vyssh. Uchebn. Zaved. Khim. Khim. Tekhnol. 2017. V. 60. N 3. P. 97-99.

An “unreasonable effectiveness” of Hilbert transform for the transition phase behavior in an Aharonov–Bohm two-path interferometer

The recent phase shift data of Takada et al. (Phys. Rev. Lett. 113 (2014) 126601) for a two level system are reconstructed from their current intensity curves by the method of Hilbert transform, for which the underlying Physics is the principle of causality. An introductory algebraic model illustrates pedagogically the working of the method and leads to newly derived relationships involving phenomenological parameters, in particular for the sign of the phase slope between the resonance peaks. While the parametrization of the experimental current intensity data in terms of a few model parameters shows only a qualitative agreement for the phase shift, due to the strong impact of small, detailed variations in the experimental intensity curve on the phase behavior, the numerical Hilbert transform yields a satisfactory reproduction of the phase.

Topology and internal structure of PEGylated lipid nanocarriers for neuronal transfection: synchrotron radiation SAXS and cryo-TEM studies

Towards potential treatment of neurodegenerative disorders by nanomedicine gene therapy, a nonviral gene delivery system is created by complexation of novel PEGylated cationic lipid assemblies and a plasmid DNA encoding for the protein brain-derived neurotrophic factor (BDNF). The generated monoolein-based liquid crystalline nanocarriers for BDNF gene transfer are characterized by means of small-angle X-ray scattering (SAXS) and cryogenic transmission electron microscopy (cryo-TEM) techniques. The complexation of the BDNF plasmids (pBDNF) to the positively charged lipid nanocarriers, is directly detected by turbidity measurements. Morphologically variable populations of sterically stabilized, PEGylated multicompartment nanoobjects, with confined supercoiled DNA, are established by cryo-TEM imaging. Synchrotron radiation SAXS measurements, performed with diluted nanoparticulate dispersions, evidence the inner multilamelar structure of pear-type vesicles and flexible onion-like objects functionalized by pBDNF. The experimental SAXS intensity curves are fitted with a scattering model for multilamellar vesicles involving five lamellas. As the monoolein-based multicompartment nanocarriers can strongly affect the organization of targeted membranes, the obtained structural data are of fundamental interest for improvement of brain-targeted gene delivery and understanding of cellular internalization mechanisms of nanocarriers in neuronal transfection studies.

An alternative gas-phase electron diffraction and quantum chemical study of nitroethane

The results of alternative gas-phase electron diffraction (GED) study of nitroethane are compared with those reported in the previous study by Tarasov et al. [1]. A fairly large reliability factor ( R = 6.1%) obtained in that work, even though the intensity data over the range s > 27 Å −1 were excluded from the analysis, was one of the reasons for undertaking this investigation. Our structural analysis was performed with electron diffraction patterns used by Tarasov et al. In this work, various quantum chemical models were used as initial approximations, and two sets of GED data equally well fitted to theory were obtained. For the experimental intensity curve in the range of s = 3.8–32.6 Å −1, the disagreement between the theoretical and experimental data reached R = 4.3%. The natural bond orbital (NBO) analysis and the quantum theory of atoms in molecules (QTAIM) were used to reveal the reasons of a low barrier to rotation of nitro group.

LEED and DFT Study of the Quasihexagonal TiO2 Structure on Cu(001)

Reactive deposition of Ti on the Cu(001) surface saturated with chemisorbed oxygen results in the formation of an ordered ultrathin film with a slightly distorted hexagonal (quasihexagonal) unit cell. We find that, under appropriate substrate temperature, evaporation rates, and O2 pressure, it is possible to cover the whole substrate surface with the TiO2 quasihexagonal phase. An O−Ti−O trilayer model for the (quasi) hexagonal structure is consistent with angle scanned XPD data relative to the Ti 2p signal and with the LEED I−V experimental intensity curves. From a careful inspection of the LEED pattern, we derive a distortion of the hexagonal unit cell corresponding to a p(2 × 7) coincidence mesh with the substrate. The p(2 × 7) coincidence was used to model XPD data. For the analysis of LEED-IV data and for DFT calculation, the p(2 × 7) was approximated by a c(2 × 6) coincidence mesh. The c(2 × 6) approximation is very close to a p(2 × 7) in terms of lattice parameters but contains a reduced number of n...

Kinetic analysis of experimental intensity curves obtained during zeolite a synthesis using in situ 27Al NMR spectroscopy

Intensity curves obtained by in situ 27Al NMR spectroscopy during zeolite A synthesis have been used as a method for comparative kinetic investigation of zeolite crystallization. Based on inflection point analysis of intensity curves, the times of t sed for process of sedimentation, t start for initiation, and t finish for completion of process in liquid phase connected to crystallization were evaluated. Obtained values for t start and t finish indicated that the rate of processes in liquid phase, connected with gel dissolution and growth of zeolite crystal, decreases with the increase of SiO2/Al2O3 molar ratio for the same Na2O concentration. On the other hand, increase of Na2O concentration for any of specified SiO2/Al2O3 molar ratio increases the rate of the same processes.

Structural Changes of Polyacrylonitrile Film by Catalytic Effects of Nickel Particles under Carbonization Process

Structural changes of polyacrylonitrile (PAN) film, prepared by gelation/crystallization from solutions, were studied by the effect of nickel particles on the carbonization at various temperatures under argon atmosphere. The carbonized PAN at 800 °C showed thread-like structures extended from nickel particles. At 1000 °C, the thread-like structures changed to rod-like structures whose one end side was closed by a nickel particle or the aggregation. The disruption of rod-like structures occurred at 1200 °C, and the carbonization at 1400 °C provided new growth of carbon layers on the surface of spherulitic nickel particles. At 1600 °C, fibrous textures were observed as residual traces of disrupted carbon layers by the overflow of melted nickel due to the thermal expansion. The graphitization degrees for G- and T-components in the films carbonized at 1600 °C were investigated on the basis of X-ray diffraction intensity distribution from the (002) plane. The analysis was done in terms of the comparison between the experimental and theoretical diffraction intensity curves. The theoretical calculation was carried out by using a concept concerning the para-crystalline theory proposed by Hoseman and Bagchi from the viewpoint of the lattice fluctuation of the c-axis.

Analysis of pore size distribution by 2H NMR

The pore size distributions of four controlled pore glasses with mean diameters ranging from ca. 7.9 to 23.9 nm were analysed by measuring the (2)H NMR signals from the liquid fraction of confined benzene-d(6) and cyclohexane-d(12) as a function of temperature, in steps of ca. 0.1-1 K. The liquid and solid components of the adsorbates were distinguished, on the basis of the spin-spin relaxation time T(2), by employing a spin-echo sequence. The experimental intensity curves of the non-frozen liquids are well represented by a sum of two error functions. The observed melting point depressions are well represented by the simplified Gibbs-Thompson equation DeltaT = k(p)/R where R is the pore radius and k(p) is a characteristic property of the adsorbate. The k(p) value mainly affects the position of the pore size distribution curve, i.e., the mean pore radius, while the slope of the intensity curve determines the width of the distribution curve. In practice, the NMR method can only be used to determine pore sizes with reasonable accuracy in the mesoporous range unless liquids undergoing larger melting point depressions than the ones investigated so far can be found.

Catalytic effect of nickel under carbonization of polyimide films

In attempt to produce graphite films with high crystallinity by heat-treatment at temperatures lower than 3000 °C, the catalytic effect of nickel was investigated for carbonization of polyimide films prepared by mixing polyamic acid with nickel particles. The three-layered polyimide film was prepared to obtain graphite films with thickness beyond 100 μm. The middle layer composed of polyimide with nickel particles. The thickness of each layer was 50 μm and the film thickness became 150 μm. The carbonization was done at ca. 1600 °C for 5 h. The morphology of the carbonized films was observed by scanning electron microscopy. The graphitization degree was investigated on the basis of X-ray diffraction intensity distribution from the (0 0 2) plane. The analysis was done in terms of the comparison between the experimental and theoretical diffraction intensity curves. The theoretical calculation was carried out by using a concept for the para-crystalline theory proposed by Hoseman and Bagchi from the viewpoint of the lattice fluctuation of the c-axis.

1H and 2H NMR studies of benzene confined in porous solids: melting point depression and pore size distribution

The pore size distributions of four controlled pore glasses and three silica gels with nominal diameters in the range 4–24 nm were determined by measuring the 1H and 2H NMR signals from the non-frozen fraction of confined benzene and perdeuterated benzene as a function of temperature, in steps of ca. 0.1–1 K. The liquid and solid components of the adsorbate were distinguished, on the basis of the spin–spin relaxation time T 2, by employing a spin-echo sequence. The experimental intensity curves of the liquid component are well represented by a sum of two error functions. The mean melting point depression of benzene and perdeuterated benzene confined in the four controlled pore glasses, with pore radius R, follows the simplified Gibbs–Thompson equation Δ T= k p/ R with a k p value of 44 K nm. As expected, the k p value mainly determines the position of the pore size distribution curve, i.e., the mean pore radius, while the transition width determines the shape of the pore size distribution curve. The excellent agreement between the results from the 1H and 2H measurements shows that the effect of the background absorption from protons in physisorbed water and silanol groups is negligible under the experimental conditions used. The overall pore size distributions determined by NMR are in reasonable agreement with the results specified by the manufacturer, or measured by us using the N 2 sorption technique. The NMR method, which is complementary to the conventional gas sorption method, is particularly appropriate for studying pore sizes in the mesoporous range.

Dynamical low-energy electron diffraction analysis of the structure of nitric oxide on Pt( [formula omitted

The adsorption structure of NO on the Pt(1 1 1) surface at low temperature (90–130 K) was studied by dynamical analysis of low-energy electron diffraction and reflection absorption infrared spectroscopy. Three different 2×2 patterns were identified and their experimental intensity vs. voltage curves ( I– V curves) were compared with dynamically calculated I– V curves for the models including the tilted (bent) NO geometry. The differences of I– V curves can be recognized by virtue of the wider incident electron energy range than the previous dynamical analysis. The most promising interpretation is that NO occupies three sites sequentially depending on the NO coverage. In this interpretation, NO first adsorbs at the threefold fcc hollow site, next at the atop site and last at the threefold hcp hollow site. The NO saturation coverage is 0.75 ML ( 1 ML=1.5×10 −15 molecules/cm 2). The NO species at the atop site is tilted and those at both hollow sites are upright. Our new model agrees well with the recent density functional theory calculation and explains the experimental results better than the previous model, in which NO transits from the bridge site to the atop site with increasing coverage.

Structural investigation of theRh(110)−c(2×2)−CNphase

The Rh(110)-c(232)-CN phase has been examined by means of scanning tunneling microscopy ~STM! and full dynamical low-energy electron diffraction ~LEED!. From STM large c(232) domains are observed. The detailed LEED-IV structural analysis indicates that CN is located in the grooves of the ~110! surface, approximately atop second layer rhodium atoms. The CN molecules lie almost flat with their bond axes oriented perpendicular to the rhodium troughs. An outward relaxation of the first substrate interlayer distance and a strong buckling of the second Rh layer are induced by CN adsorption. Calculated and experimental intensity curves are in good agreement. An exhaustive set of other possible adsorption sites and configurations was tested and excluded on the basis of reliability-factor analysis.

Proteins in solution : from X-ray scattering intensities to interaction potentials

Biological macromolecules in solution interact with each other through medium-range (from a few Å to a few nm) interaction potentials. These potentials control the macromolecular distribution in solution, the macromolecular phase diagram and the crystallization process. We have previously shown that small angle X-ray scattering (SAXS) is a convenient tool to characterize the resulting potential, either attractive or repulsive, and to follow the changes induced by the crystallizing agents. In the present paper SAXS and simulation methods derived from statistical mechanics are coupled to determine the best fit potentials from the comparison of experimental and theoretical intensity curves. The currently used models in the colloid field are derived from the DLVO (Derjaguin, Landau, Verwey, Overbeek) potential where three types of interactions play a major role: hard sphere and electrostatic are repulsive, van der Waals are attractive. A combination of a short-range attractive potential and a coulombic repulsive indeed correctly accounts at low ionic strength for the phase diagram as a function of pH and salt concentration. The origin of the ion specificities at high ionic strength associated with the so-called “Hofmeister series” remain, however, unclear. The whole of the data demonstrates that the colloidal approach may be applied with success to protein crystallization.

Pore Structure Characterization of Porous Silica by 1H NMR Using Water, Benzene, and Cyclohexane as Probe Molecules

The pore size distribution of four commercial silica materials saturated with water have been derived from experimental 1H NMR intensity vs temperature curves (IT-curves) of the confined water. The observed melting points or transition temperatures of benzene and cyclohexane confined in the same materials are shown to be consistent with corresponding data obtained from the water IT-curves. In general, the freezing point depression (ΔT) of these fluids can be related to the pore radius R in accordance with a modified Gibbs−Thompson equation: ΔT = K/(R + d), where K and d are constants characteristic of the confined fluid. The melting point depressions of benzene and cyclohexane are shown to be more sensitive to pore radius than that of water; i.e., the two former have a larger K-value. Moreover, the average pore radius of these materials can be estimated from 1H NMR chemical shift measurements of the benzene-saturated samples. Simulation of 1H NMR spectra of benzene confined in mixtures of silica (mesopor...

An estimation of the distribution functions of doped Tb 3+ and Nd 3+ in glasses by fluorescence measurements

The distribution functions of doped Tb 3+ and Nd 3+ in silicate, germanate, borate and phosphate glasses, in which cross-relaxation among active ions plays an important role, have been estimated by fluorescence measurements. In order to analyze both the steady state and the transient fluorescence characteristics, a non-linear model for the resonant energy transfer has recently been developed. The experimental fluorescence intensity and decay curves, measured as a function of acceptor concentration, suggested a modified distribution function, which included the effect of the segregation of donors and acceptors. The number of segregated Tb 3+ ions at the second nearest neighbor position around a Tb 3+ ion was estimated to be 0.1–3.4, depending on the host glass.

Theory of two-wave mixing gain enhancement in photorefractive InP:Fe: A new mechanism of resonance

We present a new model (including both temperature and electron-hole effects) of two-beam coupling in photorefractive semiconductors under an external dc field E0. This model predicts that the exponential gain Γ can exhibit an intensity-dependent resonant behavior, yielding a π/2 phase shift of the space-charge field with respect to the incident fringe pattern. This optimum intensity strongly depends on crystal temperature but it is practically independent of the grating period. As an illustration this model is applied to InP:Fe. In this case the resonance occurs when the hole photoionization rate and the electron thermal emission rate are equal. Values of Γ as high as 20 cm−1 at 1.06 μm, for a fringe spacing of 15 μm and E0 =10 kV/cm, are predicted. The comparison between theory and experimental data requires taking into account the variation of the pump intensity throughout the sample (due to optical absorption), which reduces the volume where the resonance condition is fulfilled; in this way a satisfactory fit of the experimental gain versus intensity curve has been obtained. The characteristics of this new resonance mechanism suggest several gain enhancement techniques which are briefly discussed. In particular, an increase of Γ by using an additional incoherent backward propagating beam is predicted and experimentally demonstrated.

Structure studies of non-crystalline materials by electron diffraction

The ability of electron diffraction to determine the structure of non-crystalline materials has been critically revised on the basis of the main sources of error: the premature temination of the experimental intensity curve and the problems associated with the elimination of the inelastically scattered intensity. A method of studying the problem is presented and the efficacy of the most representative procedures for reducing errors in the final correlation functions is checked.