Anomalous Scattering Research Articles

Identifying the location of Cu ions in nanostructured SAPO-5 molecular sieves and its impact on the redox properties.

Combining X-ray Absorption Fine Spectroscopy (XAFS) with Anomalous Small-Angle X-ray Scattering (ASAXS) determines the location of Cu2+ ions in silicoaluminophosphate (SAPO-5) frameworks prepared by hydrothermal crystallization or impregnation. As expected, for the hydrothermally prepared sample, incorporation in the SAPO-5 framework was observed. For the first time preferential location of Cu2+ ions at the inner and outer surfaces of the framework is determined. Temperature-Programmed Reduction (TPR) and X-ray Photoelectron Spectroscopy (XPS) investigations demonstrated that such Cu2+ is stable in an argon (Ar) atmosphere up to 550 °C and can only be reduced under a hydrogen atmosphere. In contrast, Cu2+ deposited by impregnation on the pure SAPO-5 framework can be easily reduced to Cu+ in an Ar atmosphere. At lower Cu amounts, mononuclear tetrahedrally coordinated Cu species were formed which are relatively stable in the monovalent form. In contrast, at higher Cu amounts, CuO particles were found which change easily between the mono- and bivalent species.

Anomalous Light Scattering by Pure Seawater

The latest model for light scattering by pure seawater was used to investigate the anomalous behavior of pure water. The results showed that water exhibits a minimum scattering at 24.6 °C, as compared to the previously reported values of minimum scattering at 22 °C or maximum scattering at 15 °C. The temperature corresponding to the minimum scattering also increases with the salinity, reaching 27.5 °C for S = 40 psu.

Nanometer-Sized Crystalline Clusters of IGZO Films Determined from the Grazing Incidence X-ray Scattering and Anomalous X-ray Scattering Data Combined with Reverse Monte Carlo Simulations

Grazing incidence X-ray scattering measurements have been carried out on c-axis aligned crystalline-indium gallium zinc oxide (CAAC-IGZO) film and nanocrystalline category-indium gallium zinc oxide (NC-IGZO) film and the following results were obtained: (1) the characteristic layered structure of the IGZO crystal did not hold its shape and the X-ray scattering profile showed only a relatively sharp first peak at the wave vector (Q) = 21.8 for CAAC film and 23.1 nm−1 for NC film, respectively, and additional weak broad peaks were observed at a higher angle. (2) In the case of the CAAC film, tiny peaks were observed at Q = 7 and 14 nm−1, corresponding to the positions of the 003 and 006 reflections, respectively, of the IGZO crystal. Such tiny peaks were not detected in the case of NC film but the asymmetry of the first peak at the low angle side was clearly observed. (3) These structural features implied that more than three polyhedral units, such as InOx (x = 4–6), GaOy (y = 4–6), and ZnOz (z = 4–6), were likely to coexist. It is appropriate to call this structural feature as cluster-1. (4) A composite-type structure formed by combining these polyhedral units is also likely to exist and leads to middle-range ordering. This structure is called cluster-2. The size of such cluster-2 has been estimated to be 2.2 nm for CAAC film and 1.8 nm for NC film using the measured pair distribution function. To gain insights into the structural features of IGZO films, realistic atomic-scale models were obtained to fit not only the ordinary interference function of grazing incidence X-ray scattering but also the environmental interference function of the anomalous X-ray scattering (AXS) with Zn-absorption edge using reverse Monte Carlo (RMC) simulation. (5) The resultant models indicated the complex and irregular atomic arrangements of two types of IGZO films, which are well characterized by nanometer-sized crystalline clusters. This characteristic feature may be referred to as crystalline–cluster–composite (triple C) structure.

Cone-Shaped Emissions in Cholesteric Liquid Crystal Lasers: The Role of Anomalous Scattering in Photonic Structures

The out-of-normal emission in cholesteric liquid-crystal lasers is studied experimental and theoretically. Apart from the well-known dominant laser in the direction of the helix axis, three other types of radiation, with cone-shaped spatial patterns, are identified and characterized. The physical mechanisms responsible for the different emissions are clarified. One of the radiations is a weak colorful lasing emission whose wavelength changes continuously depending on the propagation direction. The wavelengths of the other two radiations take place at the long-wavelength and short-wavelength edges of the photonic bandgap. These emissions are attributed to an anomalous scattering phenomenon that gives rise to energy transfer from the main laser beam to some specific directions where the amount of final photonic states is high. An expression for the scattering cross section, reminiscent of Fermi’s golden rule for spontaneous emission in photonic structures, is proposed. Some other phenomena independent of th...

Cardiac risk and MCNP/SISCODES doses in RT of the left internal mammary chain with photon and electron portals.

The present study evaluated the increment of cardiac risk (CR) and absorbed dose in radiotherapy of the internal mammary chain (IMC), in particular with photon portals of 4 6 MV, and cobalt therapy (Co60); and, electron portals of 8, 12 and 16 MeV applied in the left breast, considering the adoption of a combined photon (16 Gy) and electron (30 Gy) protocols. The modified ICRP-reference female model of 60 kg, 163 cm and 43 years of age, coil RCP-AF, was modelled. The MCNP6/SICODES codes were employed, where the spatial dose distributions and dose-volume histograms were generated. Toxicity limits and a CR model were considered. CR associated with the 6 MV, 4 MV and Co60 portals increased 41.1; 40.6 and 34.5%, respectively; while, in 8, 12 and 16 MeV portals, they were 5.0, 32.5 and 49.2%, respectively. High anomalous scatter radiation from electron portals was found in the left lung providing an average dose of 3.3-5.0 Gy. To RCP-AF, the Co60 portal for IMC-RT presented more attractive dose distribution, whose 16 Gy for photon-component produced less CR increase, 5% lower than the other photon portals. Considering electron portals, the smallest CR increase was produced by 8 MeV portal while 12-16 MeV made the risk higher. There is a call for a less hardened energetic spectrum in order to reduce CR; however, holding suitable IMC penetration. A combined Co60/8-12 MeV may bring benefits, reducing CR. The lowest risk was found to 46 Gy electron portals exclusively.

Effects of the Electronic Spin–Orbit Interaction on the Anomalous Asymmetric Scattering of the Spin-Polarized He+ Beam with Paramagnetic Target Materials II. Partial Wave Representation

The scattering of an electron-spin-polarized 4He+ beam on paramagnetic materials has an anomalously large asymmetric scattering component (ASC) around 10%, which is 104 times that expected from the...

Probabilistic Estimate of |Foa| from FEL Data

The method of the joint probability distribution function was applied in order to estimate the normal structure factor amplitudes of the anomalous scatterer substructure in a FEL experiment. The two-wavelength case was examined. In this, the prior knowledge of the moduli | F 1 + | , | F 1 − | , | F 2 + | , | F 2 − | was used to predict the value of | F 0 a | , which is the structure factor amplitude arising from the normal scattering of the heavy atom anomalous scatterers. The mathematical treatment provides a solid theoretical basis for the RIP (Radiation-damage Induced Phasing) method, which was originally proposed in order to take the radiation damage induced by synchrotron radiation sources into account. This was further adapted to exploit FEL data, where the crystal damage is usually more massive.

Elucidation of Spatial Distribution of Hydrophobic Aromatic Compounds Encapsulated in Polymer Micelles by Anomalous Small-Angle X-ray Scattering.

Spatial distribution of bromobenzene (BrBz) and 4-bromophenol (BrPh) as hydrophobic aromatic compounds incorporated in polymer micelles with vesicular structure consisting of poly(ethylene glycol)-b-poly(tert-butyl methacrylate) (PEG-b-PtBMA) in aqueous solution is investigated by anomalous small-angle X-ray scattering (ASAXS) analyses near Br K edge. Small-angle X-ray scattering (SAXS) intensities from PEG-b-PtBMA micelles containing BrBz and BrPh were decreased as the energy of incident X-ray approached to Br K edge corresponding to the energy dependence of anomalous scattering factor of Br. The analysis for the energy dependence of SAXS profiles from the PEG-b-PtBMA micelles containing BrBz revealed that BrBz molecules were located in hydrophobic layer of PEG-b-PtBMA micelles. On the contrary, it was found by ASAXS that BrPh existed not only in the hydrophobic layer but also in the shell layer. Since ASAXS analysis successfully accomplished to visualize the spatial distribution of hydrophobic molecules in polymer micelles, it should be expected to be a powerful tool for characterization of drug delivery vehicles.

The Significance of Solutions Obtained from Ill-Posed Systems of Linear Equations Constituted by Synchrotron Radiation Based Anomalous Small-Angle X-Ray Scattering

Synchrotron radiation based experimental techniques known as Anomalous Small-Angle X-ray Scattering (ASAXS) provide deep insight into the nanostructure of uncountable material systems in condensed matter research i.e. solid state physics, chemistry, engineering and life sciences thereby rendering the origin of the macroscopic functionalization of the various materials via correlation to its structural architecture on a nanometer length scale. The techniques constitute a system of linear equations, which can be treated by matrix theory. The study aims to analyze the significance of the solutions of the stated matrix equations by use of the so-called condition numbers first introduced by A. Turing, J. von Neumann and H. Goldstine. Special attention was given for the comparison with direct methods i.e. the Gaussian elimination method. The mathematical roots of ill-posed ASAXS equations preventing matrix inversion have been identified. In the framework of the theory of von Neumann and Goldstine the inversion of certain matrices constituted by ASAXS gradually becomes impossible caused by non-definiteness. In Turing’s theory which starts from more general prerequisites, the principal minors of the same matrices approach singularity thereby imposing large errors on inversion. In conclusion both theories recommend for extremely ill-posed ASAXS problems avoiding inversion and the use of direct methods for instance Gaussian elimination.

The signal-to-noise ratio in SAD experiments

ABSTRACTDe novo single-wavelength anomalous dispersion (SAD) determination of macromolecular structures requires accurate measurement of anomalous signal from naturally occurring (S, P, Ca, etc.) or incorporated (Se, Hg, etc.) anomalous scatterers. The quality and the level of the anomalous signal in SAD datasets can be assessed using, as an indicator, the average anomalous signal-to-noise level ⟨|ΔIanom|/σ(ΔI)⟩ based on intensities or ⟨|ΔFanom|/σ(ΔF)⟩ based on amplitudes. The value for the average anomalous signal-to-noise for a successful SAD experiment is a matter of debate given its high variability from one SAD experiment to another. We present a mathematical model relating the ⟨|ΔIanom|/σ(ΔI)⟩ to the overall final ⟨I/σ(I)⟩, necessary for successful SAD phasing. By statistical analysis of the data from 115 successful native SAD experiments, as available in the PDB, we show that the experimental values of ⟨|ΔIanom|/σ(ΔI)⟩ follow a Gamma distribution with an average value of 1.2 ± 0.3. This mathematical model allows a-priori prediction of the overall ⟨I/σ(I)⟩, necessary for successful SAD phasing given the description of the sample expressed. The results reported here are of general applicability to any phasing experiment involving the measurement of anomalous signal from any anomalous scatterer or X-ray source, including X-FEL data.

Rapid cadmium SAD phasing at the standard wavelength (1 Å).

Cadmium ions can be effectively used to promote crystal growth and for experimental phasing. Here, the use of cadmium ions as a suitable anomalous scatterer at the standard wavelength of 1 Å is demonstrated. The structures of three different proteins were determined using cadmium single-wavelength anomalous dispersion (SAD) phasing. Owing to the strong anomalous signal, the structure of lysozyme could be automatically phased and built using a very low anomalous multiplicity (1.1) and low-completeness (77%) data set. Additionally, it is shown that cadmium ions can easily substitute divalent ions in ATP-divalent cation complexes. This property could be generally applied for phasing experiments of a wide range of nucleotide-binding proteins. Improvements in crystal growth and quality, good anomalous signal at standard wavelengths (i.e. no need to change photon energy) and rapid phasing and refinement using a single data set are benefits that should allow cadmium ions to be widely used for experimental phasing.

Effects of the Electronic Spin–Orbit Interaction on the Anomalous Asymmetric Scattering of the Spin-Polarized 4He+ Beam with Paramagnetic Target Materials

The scattering of the electron-spin-polarized 4He+ beam on paramagnetic materials has an anomalously large asymmetric scattering component (ASC) around 5%, which is 104 of that expected from the spin–orbit coupling (SOC) for the potential of the target nucleus. In addition, the ASC of some materials (for example, Au and Pt) changes sign near the scattering angle (θ) of 90° unlike the result predicted by using the potential scattering theory. When the 4He+ approaches the target, virtual electron-transfer (ET) excitations between them occur. The effects of the SOC of electrons (SOEs) on the target atom in the ET intermediate state are studied within the frame of the lowest-order perturbation theory about the ET process. The ASC is caused through the combination of the quantum development of electron orbital states under the SOEs and the He nucleus motion in the intermediate state because the preferred orbital states for the ET depend on the position of the He nucleus. It is shown by a numerical calculation ...

The hidden treasure in your data: phasing with unexpected weak anomalous scatterers from routine data sets.

Single-wavelength anomalous dispersion (SAD) utilizing anomalous signal from native S atoms, or other atoms with Z ≤ 20, generally requires highly redundant data collected using relatively long-wavelength X-rays. Here, the results from two proteins are presented where the anomalous signal from serendipitously acquired surface-bound Ca atoms with an anomalous data multiplicity of around 10 was utilized to drive de novo structure determination. In both cases, the Ca atoms were acquired from the crystallization solution, and the data-collection strategy was not optimized to exploit the anomalous signal from these scatterers. The X-ray data were collected at 0.98 Å wavelength in one case and at 1.74 Å in the other (the wavelength was optimized for sulfur, but the anomalous signal from calcium was exploited for structure solution). Similarly, using a test case, it is shown that data collected at ∼1.0 Å wavelength, where the f'' value for sulfur is 0.28 e, are sufficient for structure determination using intrinsic S atoms from a strongly diffracting crystal. Interestingly, it was also observed that SHELXD was capable of generating a substructure solution from high-exposure data with a completeness of 70% for low-resolution reflections extending to 3.5 Å resolution with relatively low anomalous multiplicity. Considering the fact that many crystallization conditions contain anomalous scatterers such as Cl, Ca, Mn etc., checking for the presence of fortuitous anomalous signal in data from well diffracting crystals could prove useful in either determining the structure de novo or in accurately assigning surface-bound atoms.

Solution of the structure of a calmodulin-peptide complex in a novel configuration from a variably twinned data set.

Structure determination of conformationally variable proteins can prove challenging even when many possible molecular-replacement (MR) search models of high sequence similarity are available. Calmodulin (CaM) is perhaps the best-studied archetype of these flexible proteins: while there are currently ∼450 structures of significant sequence similarity available in the Protein Data Bank (PDB), novel conformations of CaM and complexes thereof continue to be reported. Here, the details of the solution of a novel peptide-CaM complex structure by MR are presented, in which only one MR solution of marginal quality was found despite the use of 120 different search models, an exclusivity enhanced by the presence of a high degree of hemihedral twinning (overall refined twin fraction = 0.43). Ambiguities in the initial MR electron-density maps were overcome by using MR-SAD: phases from the MR partial model were used to identify weak anomalous scatterers (calcium, sulfur and chloride), which were in turn used to improve the phases, automatically rebuild the structure and resolve sequence ambiguities. Retrospective analysis of consecutive wedges of the original data sets showed twin fractions ranging from 0.32 to 0.55, suggesting that the data sets were variably twinned. Despite these idiosyncrasies and obstacles, the data themselves and the final model were of high quality and indeed showed a novel, nearly right-angled conformation of the bound peptide.

Anomalous Light Scattering by Topological PT-symmetric Particle Arrays.

Robust topological edge modes may evolve into complex-frequency modes when a physical system becomes non-Hermitian. We show that, while having negligible forward optical extinction cross section, a conjugate pair of such complex topological edge modes in a non-Hermitian -symmetric system can give rise to an anomalous sideway scattering when they are simultaneously excited by a plane wave. We propose a realization of such scattering state in a linear array of subwavelength resonators coated with gain media. The prediction is based on an analytical two-band model and verified by rigorous numerical simulation using multiple-multipole scattering theory. The result suggests an extreme situation where leakage of classical information is unnoticeable to the transmitter and the receiver when such a -symmetric unit is inserted into the communication channel.

Identification of metal sources in Geogas from the Wangjiazhuang copper deposit, Shandong, China: Evidence from lead isotopes

The Geogas survey has been confirmed to be a useful geochemical pathfinder in prospecting for mineral deposits concealed beneath various types and thicknesses of overburden. To understand the sources of metals in Geogas, the lead isotopes were chosen as tracers. The Pb isotope ratios in soil, host rocks and ores were determined following separation and purification by Nu Plasma HR Ionization Mass Spectrometer and those in Geogas samples were analyzed by HR-ICP-MS (High Resolution Inductively Coupled Plasma-Mass Spectronmetry) (Element 2) and iCAP Q-ICP-MS (Quadrupole Inductively Coupled Plasma-Mass Spectronmetry) with optimized operating parameters. The utilization of HR-ICP-MS and iCAP Q-ICP-MS can be effective in determining extremely low levels of Pb isotopes and make great progress in analytical precision and sensitivity to render the test data and experimental results more convincing. The results of this study of different samples collected at the Wangjiazhuang Cu deposit show that Pb isotope ratios of Geogas background samples are apparently different from those of various media (soil, host rocks and ores) in the vicinity of the ore bodies. The Pb isotope ratios in Geogas anomalous samples are quite distinct from those in Geogas background samples. The Pb isotope ratios of Geogas anomalous samples scatter close to ores. It is assumed that the anomalous Pb in Geogas samples came mainly from deeply concealed mineral deposits, this research provides much more reliable evidence for the explanation of Geogas anomalies and further demonstrates that the Geogas technique is a viable tool to identify deeply buried mineralization under exotic overburden.

Effect of protective coating on random birefringence variations in anisotropic optical fibres in response to temperature changes

This paper examines for the first time the nature of an anomalous scatter in the birefringence beat length in an anisotropic silica fibre upon changes in its temperature. The effect has been studied by a conventional interferometric technique, using a spectrum analyser. The dispersion of the scatter in the beat length has been shown to be considerably higher at short fibre lengths, which is due to the effect of the protective coating. To interpret the observed effects, a physical model has been proposed which considers random centres, such as microbends, which form and disappear in the protective coating of the fibre in response to temperature changes. The random nature of such local centres may lead to unpredictable changes in the birefringence of anisotropic fibres and, hence, to changes in the sensitivity and accuracy of Faraday effect current sensors.

On the influence of crystal size and wavelength on native SAD phasing.

Native SAD is an emerging phasing technique that uses the anomalous signal of native heavy atoms to obtain crystallographic phases. The method does not require specific sample preparation to add anomalous scatterers, as the light atoms contained in the native sample are used as marker atoms. The most abundant anomalous scatterer used for native SAD, which is present in almost all proteins, is sulfur. However, the absorption edge of sulfur is at low energy (2.472 keV = 5.016 Å), which makes it challenging to carry out native SAD phasing experiments as most synchrotron beamlines are optimized for shorter wavelength ranges where the anomalous signal of sulfur is weak; for longer wavelengths, which produce larger anomalous differences, the absorption of X-rays by the sample, solvent, loop and surrounding medium (e.g. air) increases tremendously. Therefore, a compromise has to be found between measuring strong anomalous signal and minimizing absorption. It was thus hypothesized that shorter wavelengths should be used for large crystals and longer wavelengths for small crystals, but no thorough experimental analyses have been reported to date. To study the influence of crystal size and wavelength, native SAD experiments were carried out at different wavelengths (1.9 and 2.7 Å with a helium cone; 3.0 and 3.3 Å with a helium chamber) using lysozyme and ferredoxin reductase crystals of various sizes. For the tested crystals, the results suggest that larger sample sizes do not have a detrimental effect on native SAD data and that long wavelengths give a clear advantage with small samples compared with short wavelengths. The resolution dependency of substructure determination was analyzed and showed that high-symmetry crystals with small unit cells require higher resolution for the successful placement of heavy atoms.

Studies of the B-Z transition of DNA: The temperature dependence of the free-energy difference, the composition of the counterion sheath in mixed salt, and the preparation of a sample of the 5'-d[T-(m(5) C-G)12 -T] duplex in pure B-DNA or Z-DNA form.

It is often envisioned that cations might coordinate at specific sites of nucleic acids and play an important structural role, for instance in the transition between B-DNA and Z-DNA. However, nucleic acid models explicitly devoid of specific sites may also exhibit features previously considered as evidence for specific binding. Such is the case of the "composite cylinder" (or CC) model which spreads out localized features of DNA structure and charge by cylindrical averaging, while sustaining the main difference between the B and Z structures, namely the better immersion of the B-DNA phosphodiester charges in the solution. Here, we analyze the non-electrostatic component of the free-energy difference between B-DNA and Z-DNA. We also compute the composition of the counterion sheath in a wide range of mixed-salt solutions and of temperatures: in contrast with the large difference of composition between the B-DNA and Z-DNA forms, the temperature dependence of sheath composition, previously unknown, is very weak. In order to validate the model, the mixed-salt predictions should be compared to experiment. We design a procedure for future measurements of the sheath composition based on Anomalous Small-Angle X-ray Scattering and complemented by (31) P NMR. With due consideration for the kinetics of the B-Z transition and for the capacity of generating at will the B or Z form in a single sample, the 5'-d[T-(m(5) C-G)12 -T] 26-mer emerges as a most suitable oligonucleotide for this study. Finally, the application of the finite element method to the resolution of the Poisson-Boltzmann equation is described in detail. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 369-384, 2016.

Efficient merging of data from multiple samples for determination of anomalous substructure.

Merging of data from multiple crystals has proven to be useful for determination of the anomalously scattering atomic substructure for crystals with weak anomalous scatterers (e.g. S and P) and/or poor diffraction. Strategies for merging data from many samples, which require assessment of sample isomorphism, rely on metrics of variability in unit-cell parameters, anomalous signal correlation and overall data similarity. Local scaling, anomalous signal optimization and data-set weighting, implemented in phenix.scale_and_merge, provide an efficient protocol for merging data from many samples. The protein NS1 was used in a series of trials with data collected from 28 samples for phasing by single-wavelength anomalous diffraction of the native S atoms. The local-scaling, anomalous-optimization protocol produced merged data sets with higher anomalous signal quality indicators than did standard global-scaling protocols. The local-scaled data were also more successful in substructure determination. Merged data quality was assessed for data sets where the multiplicity was reduced in either of two ways: by excluding data from individual crystals (to reduce errors owing to non-isomorphism) or by excluding the last-recorded segments of data from each crystal (to minimize the effects of radiation damage). The anomalous signal was equivalent at equivalent multiplicity for the two procedures, and structure-determination success correlated with anomalous signal metrics. The quality of the anomalous signal was strongly correlated with data multiplicity over a range of 12-fold to 150-fold multiplicity. For the NS1 data, the local-scaling and anomalous-optimization protocol handled sample non-isomorphism and radiation-induced decay equally well.