Anomalous Diffraction Research Articles

Making a difference in multi-data-set crystallography: simple and deterministic data-scaling/selection methods.

Phasing by single-wavelength anomalous diffraction (SAD) from multiple crystallographic data sets can be particularly demanding because of the weak anomalous signal and possible non-isomorphism. The identification and exclusion of non-isomorphous data sets by suitable indicators is therefore indispensable. Here, simple and robust data-selection methods are described. A multi-dimensional scaling procedure is first used to identify data sets with large non-isomorphism relative to clusters of other data sets. Within each cluster that it identifies, further selection is based on the weighted ΔCC1/2, a quantity representing the influence of a set of reflections on the overall CC1/2 of the merged data. The anomalous signal is further improved by optimizing the scaling protocol. The success of iterating the selection and scaling steps was verified by substructure determination and subsequent structure solution. Three serial synchrotron crystallography (SSX) SAD test cases with hundreds of partial data sets and one test case with 62 complete data sets were analyzed. Structure solution was dramatically simplified with this procedure, and enabled solution of the structures after a few selection/scaling iterations. To explore the limits, the procedure was tested with much fewer data than originally required and could still solve the structure in several cases. In addition, an SSX data challenge, minimizing the number of (simulated) data sets necessary to solve the structure, was significantly underbid.

Epitaxial L1-FeNi films with high degree of order and large uniaxial magnetic anisotropy fabricated by denitriding FeNiN films

L10-orderd FeNi alloy films with a high degree of order (S) and a large uniaxial magnetic anisotropy energy (Ku) were realized by denitriding FeNiN films. FeNiN films with the a-axis perpendicular to the film plane were epitaxially grown on SrTiO3 (001) substrates by molecular beam epitaxy by changing the growth temperatures (TS) to 200, 250, and 350 °C. The a-axis oriented epitaxial L10-FeNi films were fabricated by annealing the FeNiN films in a H2 gas atmosphere at 300 °C. S and Ku of the denitrided L10-FeNi films were characterized by anomalous x-ray diffraction using synchrotron radiation and magnetic torque measurements, respectively. A high S of 0.87 and a Ku of 5.9 × 105 J/m3 were realized in the L10-FeNi film with a TS of 350 °C. This high S value exceeds the values reported on L10-FeNi to date, but the Ku value was comparable to those of c-axis oriented L10-FeNi films with S ∼ 0.5 grown by alternate monoatomic deposition of Fe and Ni layers. A possible origin for the suppressed macroscopic Ku in a-axis oriented L10-FeNi films is discussed, and denitriding FeNiN is a promising method for the fabrication of L10-FeNi with a high S and a large Ku.

Noise source location and scaling of subsonic upper-surface blowing

This paper deals with the topic of upper surface blowing noise. Using a model-scale rectangular nozzle of an aspect ratio of 10 and a sharp trailing edge, detailed noise contours were acquired with and without a subsonic jet blowing over a flat surface to determine the noise source location as a function of frequency. Additionally, velocity scaling of the upper surface blowing noise was carried out. It was found that the upper surface blowing increases the noise significantly. This is a result of both the trailing edge noise and turbulence downstream of the trailing edge, referred to as wake noise in the paper. It was found that low-frequency noise with a peak Strouhal number of 0.02 originates from the trailing edge whereas the high-frequency noise with the peak in the vicinity of Strouhal number of 0.2 originates near the nozzle exit. Low frequency (low Strouhal number) follows a velocity scaling corresponding to a dipole source where as the high Strouhal numbers as quadrupole sources. The culmination of these two effects is a cardioid-shaped directivity pattern. On the shielded side, the most dominant noise sources were at the trailing edge and in the near wake. The trailing edge mounting geometry also created anomalous acoustic diffraction indicating that not only is the geometry of the edge itself important, but also all geometry near the trailing edge.

Spontaneous diametric-drive acceleration initiated by a single beam in a photonic lattice.

We demonstrate that a single Gaussian-like beam can self-bend during nonlinear propagation in a uniform photonic lattice. The two components of the beam experiencing normal and anomalous diffractions spontaneously separate and form a pair in a diametric-drive acceleration due to nonlinear action. Such a diametric drive generally describes a jointly accelerating behavior of two beams analogous to positive- and negative-mass objects. The influences of the initial momentum of the input beam and the nonlinear strength are considered in this process. We further realize a self-bending propagation for a partially coherent light beam and discuss the impact of incoherence on the acceleration strength.

Structure of a gut microbial diltiazem-metabolizing enzyme suggests possible substrate binding mode

When administrated orally, the vasodilating drug diltiazem can be metabolized into diacetyl diltiazem in the presence of Bacteroides thetaiotaomicron, a human gut microbe. The removal of acetyl group from the parent drug is carried out by the GDSL/SGNH-family hydrolase BT4096. Here the crystal structure of the enzyme was solved by mercury soaking and single-wavelength anomalous diffraction. The protein folds into two parts. The N-terminal part comprises the catalytic domain which is similar to other GDSL/SGNH hydrolases. The flanking C-terminal part is made up of a β-barrel subdomain and an α-helical subdomain. Structural comparison shows that the catalytic domain is most akin to acetyl-xylooligosaccharide esterase and allows a plausible binding mode of diltiazem to be proposed. The β-barrel subdomain is similar in topology to the immunoglobulin-like domains, including some carbohydrate-binding modules, of various bacterial glycoside hydrolases. Consequently, BT4096 might originally function as an oligosaccharide deacetylase with additional subdomains that could enhance substrate binding, and it acts on diltiazem just by accident.

Unusual Moiré superlattices in exfoliated μm-thin HOPG lamellae: An angular-diffraction study

The observation of intrinsic magnetic correlation phenomena in presence of Moiré-superlattices in twisted-bilayer-graphene, double-bilayer-graphene and graphite has recently attracted important attention. By employing high resolution transmission electron microscopy (HRTEM), in this study we have investigated μm-thin HOPG-lamellae with unusual Moiré-superlattices. Anomalous large periodicities of ~80 nm and ~40 nm, possibly corresponding to θmisfit of 0.18° and 0.35° are reported.X-ray-rocking-curve-analyses, evidenced the presence of non-monotonic signals, a clear indicator of dislocation-rich-properties. Selective area electron diffraction (SAED) of the superlattice further revealed the presence of anomalous doubled diffraction patterns. The angular-dependence of SAED with sample-tilt from 0° to 0.93° evidenced an increase in the pattern-intensity up to a maximum for sample-tilt of 0.33°. Disappearance (of SAED-doubled-pattern and Moiré-superlattice) was found for 0.66° and 0.93° tilt. Re-appearance was further verified, by taking the sample back to 0.33° tilt. Raman-spectroscopy and scanning electron microscopy supported the observed results, revealing 1) presence of D and D’ band signals and 2) absence of sample oxidation.

Anomalous X-ray scattering study on oxidized TbxDy1-xFe2-y thin films: Influence of thermal annealing on the oxide composition

Thin films of the ternary compound TbxDy1-xFe2-y were prepared by DC magnetron sputtering from a TbDyFe alloy target with the composition same as Terfenol-D alloy (Tb0.32Dy0.68Fe1.92) onto 400 °C Si (001) substrates. The influence of post annealing temperature at 550 °C, 700 °C or 850 °C for 6 h are studied systematically on a series of TbxDy1-xFe2-y samples. However, the annealing process leads to the incorporation of oxygen impurity into the thin film. To understand the effects of annealing temperature on the microstructural and crystalline degree of oxidation of RFe2 thin film, different characterisation techniques such as anomalous X-ray scattering and electron probe micro-analyzer were performed. These measurements show that Fe clusters phase gets segregated from the bulk matrix during annealing at 550 °C and 850 °C but do not segregate while annealing at 700 °C. In this work, we present an anomalous X-ray diffraction measurement on TbxDy1-xFe2-y to determine the composition ratio of rare earth oxides in thin film and compositional analysis.

Heterotrimetallic Mixed‐Valent Molecular Precursors Containing Periodic Table Neighbors: Assignment of Metal Positions and Oxidation States

AbstractA known trinuclear structure was used to design the heterobimetallic mixed‐valent, mixed‐ligand molecule [CoII(hfac)3−Na−CoIII(acac)3] (1). This was used as a template structure to develop heterotrimetallic molecules [CoII(hfac)3−Na−FeIII(acac)3] (2) and [NiII(hfac)3−Na−CoIII(acac)3] (3) via isovalent site‐specific substitution at either of the cobalt positions. Diffraction methods, synchrotron resonant diffraction, and multiple‐wavelength anomalous diffraction were applied beyond simple structural investigation to provide an unambiguous assignment of the positions and oxidation states for the periodic table neighbors in the heterometallic assemblies. Molecules of 2 and 3 are true heterotrimetallic rather than a statistical mixture of two heterobimetallic counterparts. Trinuclear platform 1 exhibits flexibility in accommodating a variety of di‐ and trivalent metals, which can be further utilized in the design of molecular precursors for the NaMM′O4 functional oxide materials.

Heterotrimetallic Mixed‐Valent Molecular Precursors Containing Periodic Table Neighbors: Assignment of Metal Positions and Oxidation States

A known trinuclear structure was used to design the heterobimetallic mixed-valent, mixed-ligand molecule [CoII (hfac)3 -Na-CoIII (acac)3 ] (1). This was used as a template structure to develop heterotrimetallic molecules [CoII (hfac)3 -Na-FeIII (acac)3 ] (2) and [NiII (hfac)3 -Na-CoIII (acac)3 ] (3) via isovalent site-specific substitution at either of the cobalt positions. Diffraction methods, synchrotron resonant diffraction, and multiple-wavelength anomalous diffraction were applied beyond simple structural investigation to provide an unambiguous assignment of the positions and oxidation states for the periodic table neighbors in the heterometallic assemblies. Molecules of 2 and 3 are true heterotrimetallic rather than a statistical mixture of two heterobimetallic counterparts. Trinuclear platform 1 exhibits flexibility in accommodating a variety of di- and trivalent metals, which can be further utilized in the design of molecular precursors for the NaMM'O4 functional oxide materials.

Structural Basis of 7‐Deazaguanine Modification of DNA in Bacteria and Phage

Two important modifications of tRNA, the 7‐deazaguanine nucleosides queuosine (Q) and archaeosine (G+), are biosynthesized from GTP in bacteria and archaea, respectively, in a well characterized multi‐enzyme pathway leading to the shared advanced intermediate, 7‐cyano‐7‐deazaguanine (preQ0). In bacteria, preQ0 is converted to an aminomethyl derivative that is then inserted in tRNA by the bacterial tRNA‐guanine transglycosylase (TGT) enzyme. In archaea, preQ0 is inserted directly in tRNA by the archaeal TGT before conversion to G+. Recently, in 230 bacterial and phage genomes, a genomic island that contains a paralog of TGT was identified, which led to the discovery of Q, G+ and preQ0 deoxy derivatives in the DNA of some of these organisms. This gene cluster was renamed DpdA‐K, for “7‐deazapurine in DNA.” The G+‐modified DNA of E. coli bacteriophage 9g has been shown to resist restriction by >140 Type II restriction endonucleases (REases), consistent with a role of the modification as a defense mechanism. Recent experiments have shown that DpdA is a DNA‐guanine transglycosylase that catalyzes the insertion of preQ0 at a specific palindromic sequence in DNA. Here we report overexpression, purification, and crystallographic analysis of S. Montevideo DpdA (SmDpdA, ~47 kDa). The crystal structure, determined at 2.25‐Å resolution by multi‐wavelength anomalous diffraction methods, reveals a TIM‐barrel enzyme similar to the bacterial TGT in overall fold, active site and structural Zn2+ site. However, a large DpdA‐specific insertion in the TIM barrel provides an extended positively charged 26‐Å wide surface groove, consistent with a DNA binding surface. Free docking of a DNA duplex using the HADDOCK server places DNA to this surface in a fashion reminiscent of DNA binding to the ubiquitous Zn2+‐dependent DNA repair enzyme apurinic/apyrimidinic endonuclease IV. The structure and docking model suggest that DpdA bends its substrate DNA by 60° and flips the modification‐site guanine base out of the helix for transglycosylation. The results also inform the design of a substrate DNA duplex for future crystallization of the nucleoprotein complex.Support or Funding InformationNIGMS grant GM110588 and GM132254 to M.A.S., and The California Metabolic Research Foundation (SDSU).

Formation of stacking faults in tungsten carbide during sintering

Ultra-high density of parallel planar defects is discovered within WC grains in V-doped cemented carbide. High resolution transmission electron microscopy (HRTEM) shows that such defects are stacking faults on the {101‾0} prismatic planes. The presence of multiple stacking faults within WC grain gives rise to a series of anomalous diffraction patterns, including the streaking of diffraction spots and forbidden fractional diffraction spots. Interestingly, quantitative analysis indicates that the density of stacking faults within the V-doped sample is one order of magnitude higher than that of the Ti-doped counterpart. Because the two doped samples are processed under the same condition, we conclude that the planar defects of WC grains in V-doped samples are largely produced during the sintering of cemented carbide. Aberration-corrected TEM images suggest that the formation of stacking faults can be ascribed to the merging of independently developed WC micro-pillars. The formation of such pillars can be further explained by the segregation of V-rich precipitates at the corners between basal and prismatic planes. The current finding not only unravels a new formation mechanism of stacking faults within WC grains, but also provides a new route to design superhard cemented carbides with interlaced stacking faults by simply doping solute atoms and controlling the sintering process, other than the traditional deformation method.

Citrate-Zn/Al Layered Double Hydroxide as Adsorbent of Congo Red from Aqueous Solution

Layered double hydroxide (LDH) of Zn/Al and citrate-Zn/Al was prepared and used as an adsorbent of Congo red from aqueous solution. LDH was characterized by X-ray, FTIR, and BET analysis. Adsorption of Congo red was studied through kinetic, isotherm, and thermodynamic analyses. Zn/Al LDH has diffraction at 10.29o (003) with interlayer distance 8.59 Å and citrate-Zn/Al LDHs have anomalous diffraction at 7.57o (003) with interlayer distance 11.68 Å. The surface area of citrate-Zn/Al (40.50 m2 g-1) has higher than pristine LDH (1.97 m2 g-1). Adsorption of Congo red was conducted at pH 6 for Zn/Al LDH and at pH 8 for citrate-Zn/Al LDH. Adsorption of Congo red on both LDHs follows the pseudo-second-order kinetic model. The isotherm parameter follows the Freundlich isotherm model with maximum adsorption capacity 166.67 mg g-1 for Zn/Al and 249.99 mg g-1 for citrate-Zn/Al LDH. Adsorption of Congo red on both LDHs was classified as physical adsorption with energy 4.085-4.148 kJ mol-1.

Exploring the shear strain contribution to the uniaxial magnetic anisotropy of (Ga,Mn)As

We present an experimental and k⋅p theoretical study on the origin of the strong in-plane uniaxial magnetic anisotropy in (Ga,Mn)As layers, unexpected from the cubic crystalline structure. The symmetry lowering can be accounted for by structural or effective shear strains. We find theoretically out-of-plane and in-plane magnetic anisotropy constants being linear with the shear strain. Searching for a real shear strain arising from lattice relaxation, we perform two types of measurements: anomalous x-ray diffraction and strain-induced optical birefringence, at room temperature. Working on a strongly anisotropic (Ga,Mn)As layer, the estimated ϵxy=10−4 was not found although it lied an order of magnitude above the detection threshold. This ensemble of results indicates as unlikely a relaxation-driven uniaxial anisotropy. As previously suggested theoretically, the magnetic symmetry-lowering could instead originate from the anisotropic incorporation of Mn atoms during growth. This would yield a perfectly in-plane matched lattice, with an anisotropy that could nevertheless be modeled as an effective shear strain and modified by an external shear stress, in agreement with the existing experimental literature.

Small-Angle Scattering and Radiation Polarization by a Stretched Polymer Film with Nematic Liquid Crystal Droplets Having a Single-Domain Structure

The coefficient of directed transmittance of a stretched polymer-dispersed liquid crystal film with a defect-free single-domain liquid crystal droplet structure formed by a stretched surfactant-doped film and the polarization degree of forward-transmitted light in the visible and near-infrared spectrum ranges are studied. Results are presented for the 5CB, E7, and E44 nematic liquid crystals. Dependences of the transmission coefficient and polarizing ability of the film on the photodetector field of view are studied. Relationships allowing one to determine film parameters at which the transmission coefficient and polarizing ability of the films simultaneously reach values close to limit ones (0.5 and ±1.0, respectively) are obtained in the Foldy–Twersky and anomalous diffraction approximations.

Optical model to describe coherent transmittance of polymer dispersed liquid crystal film doped with carbon nanotubes

An optical model has been developed for analyzing the coherent transmittance of a polymer dispersed liquid crystal films doped with carbon nanotubes (CNTs) at uniform normal droplet-polymer interface anchoring. It is based on the Foldy–Twersky and anomalous diffraction approximations, Maxwell-Garnett equations, and the order parameters concept. The model allows one to analyze the electro-optical response of films depending on their thickness, the refractive indices of the liquid crystal (LC) and polymer matrix, size and concentration of the LC droplets, concentration of nanotubes, conductivities of the LC and the polymer. Experimental verification of the model is performed.

Rhombohedral Trap for Studying Molecular Oligomerization in Membranes: Application to Daptomycin

A persistent problem in the studies of membrane-active peptides, including Antimicrobial peptides and pathogenic amyloidal peptides, is the lack of methods for investigating their molecular configurations in membranes. These peptides spontaneously bind to membranes from solutions, and often form oligomers that induce changes of membrane permeability. For antimicrobials, such actions appear to relate to the antimicrobial mechanisms, but for amyloidal peptides, the oligomerization has been linked to neurodegenerative diseases.

Lipid Bilayers Influenced by Taurin and Betain

We studied the influence of natural osmolytes Taurin and Betain on the stability and fluidity of lipid model membranes. They components of daily products aim at our well-being, such as energy drinks or baby creams. We used a combination of simultaneous SAXS/WAXS/DSC measurements, being able to identify the structures, their dimensions and the phase transition temperatures. Thermal scans show morphologies similar to aqueous solution of the pure lipids, although with different dimensions and transition temperatures. In POPE, we observe structures with high curvature, and upon temperature cycling, the induction of possible cubic phases. Fully hydrated POPE hydrated with solutions of such osmolytes surprisingly lacks anomalous diffraction patterns over a wide temperature range on cooling from the hexagonal phase. The diffraction peaks in the last patterns are much less intense than at the beginning of the scan. The DSC shows a higher phase transition temperature on heating than for pure aqueous POPE, while during cooling this is not seen. DSC of POPE in on these samples shows a transition at a different temperature than purely hydrated POPE. The SAXS scan indicates a less organized stack of bilayers and the hexagonal phase, normally following the lamellar upon heating, could not be clearly seen up to 85oC. Moreover, no well-organized structure was formed during cooling. On combining SAXS/WAXS and DSC results obtained from dispersions of POPE in either aqueous solution of Taurin and Betain, one can see their effect from a structural perspective, that is, their influence on the macro organization of the self-assembled mesogenic units. Both osmolytes seem to require high temperatures (weaker interactions between headgroups of neighbouring lipids) to effectively interact with the POPE (headgroups) and influence the dispersion.

IPCAS: a direct-method-based pipeline from phasing to model building and refinement for macromolecular structure determination

A new version (2.0) of the pipeline IPCAS (Iterative Protein Crystal structure Automatic Solution) has been released, in which the program OASIS performs direct-method single-wavelength anomalous diffraction/single isomorphous replacement phasing and direct-method-aided partial-structure extension. IPCAS incorporates the widely used packages CCP4 and PHENIX for locating heavy atoms, density modification, molecular replacement, model building and refinement. Important extensions to the previous version of IPCAS include a resolution screening method for non-crystallographic symmetry searching, an alternate model-building protocol for avoiding premature convergence and direct-method image processing for electron microscopy maps, including single-particle cryo-EM maps. Moreover, a new graphical user interface is provided for controlling and real-time monitoring of the whole dual-space iterative process, which works as a plugin to CCP4i. Applications of the new IPCAS to difficult cases have yielded promising results, including `direct-method phasing and fragment extension' from weak anomalous diffraction signal data and `direct-method-aided partial-structure extension' from low-homology models.

De novo Phasing Xenons Observed in the Frog Ependymin-Related Protein

Pressurizing Xe or Kr noble gas into the protein crystal for de novo phasing has been one method of choice when the introduction of other heavy-atom compounds fails. One reason is because, unlike other heavy-atom compounds, their immobilized sites are mostly hydrophobic cavities. Previously, the structure of frog ependymin-related protein (EPDR) has been determined using a single wavelength anomalous diffraction (SAD) on a Xe-pressurized crystal. Since no report on the four Xe binding sites has been made, these sites are analyzed in this study. Of the four Xe atoms, three are found along the hydrophobic interfaces created by the two crystallographic symmetry mates of EPDR. One final Xe atom occupies a Ca2+-binding site of the native protein entirely stabilized by the polar atoms of the surrounding EDPR residues. We believe that this atypical Xe location is very unique and merits further study.

Thickness Dependence of Degree of B2 Order of Polycrystalline Co <sub>2</sub>(Mn <sub>0.6</sub>Fe <sub>0.4</sub>)Ge Heusler Alloy Films Measured by Anomalous X-Ray Diffraction and its Impacts on Current-Perpendicular-To-Plane Giant Magnetoresistance Properties

We investigated the degree of B2 order (SB2) of 4-10 nm-thick polycrystalline Co2(Mn0.6Fe0.4)Ge (CMFG) Heusler alloy films using anomalous X-ray diffraction (AXRD) and its correlation to the magnitude of current-perpendicular-to-plane giant magnetoresistive (CPP-GMR) effect. We found that SB2 of the CMFG films is degraded for the film thickness below 6 nm, which is an issue for practical applications of CPP-GMR devices such as read head sensors. Since SB2 has a thickness-dependence, the bulk spin polarization (β) of the CMFG layers is also expected to vary depending on the thickness; thus, the deduction of β using the Valet-Fert model, where β is assumed to be thickness-independent, is not valid for the CPP-GMR devices with polycrystalline CMFG layers.