X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair

DNA duplexes containing unnatural base-pair surrogates are attractive biomolecular nanomaterials with potentially beneficial photophysical or electronic properties. Herein we report the first X-ray structure of a duplex containing a phen-pair in the center of the double helix in a zipper like stacking arrangement.

In situ dehydration behavior of zeolite-like pentagonite: A single-crystal X-ray study

The structural modifications upon heating of pentagonite, Ca(VO)(Si4O10)·4H2O (space group Ccm21, a=10.3708(2), b=14.0643(2), c=8.97810(10) Å, V=1309.53(3) Å3) were investigated by in situ temperature dependent single-crystal X-ray structure refinements. Diffraction data of a sample from Poona district (India) have been measured in steps of 25 up to 250 °C and in steps of 50 °C between 250 and 400 °C. Pentagonite has a porous framework structure made up by layers of silicate tetrahedra connected by V4+O5 square pyramids. Ca and H2O molecules are extraframework occupants. Room temperature diffraction data allowed refinement of H positions. The hydrogen-bond system links the extraframework occupants to the silicate layers and also interconnects the H2O molecules located inside the channels. Ca is seven-fold coordinated forming four bonds to O of the tetrahedral framework and three bonds to extraframework H2O. The H2O molecule at O9 showing a high displacement parameter is not bonded to Ca. The dehydration in pentagonite proceeds in three steps. At 100 °C the H2O molecule at O8 was released while O9 moved towards Ca. As a consequence the displacement parameter of H2O at O9 halved compared to that at room temperature. The unit-cell volume decreased to 1287.33(3) Å3 leading to a formula with 3H2O per formula unit (pfu). Ca remained seven-fold coordinated. At 175 °C Ca(VO)(Si4O10)·3H2O transformed into a new phase with 1H2O molecule pfu characterized by doubling of the c axis and the monoclinic space group Pn. Severe bending of specific TOT angles led to contraction of the porous three-dimensional framework. In addition, H2O at O9 was expelled while H2O at O7 approached a position in the center of the channel. The normalized volume decreased to 1069.44(9) Å3. The Ca coordination reduced from seven- to six-fold. At 225 °C a new anhydrous phase with space group Pna21 but without doubling of c had formed. Release of H2O at O7 caused additional contraction of TOT angles and volume reduction (V=1036.31(9) Å3). Ca adopted five-fold coordination. During heating excursion up to 400 °C this anhydrous phase remained preserved. Between room temperature and 225 °C the unit-cell volume decreased by 21% due to dehydration. The dehydration steps compare well with the thermo-gravimetric data reported in the literature.

In situ dehydration behavior of veszelyite (Cu,Zn)2Zn(PO4)(OH)3·2H2O: A single-crystal X-ray study

The rare mixed copper-zinc phosphate mineral veszelyite (Cu,Zn)2Zn(PO4)(OH)3·2H2O space group P21/c, a = 7.5096(2), b = 10.2281(2), c = 9.8258(2) Å, β = 103.3040(10)°, V = 734.45(3) Å3 was investigated by in situ temperature-dependent single-crystal X-ray structure refinements. The atomic arrangement of veszelyite consists of an alternation of octahedral and tetrahedral sheets. The Jahn-Teller distorted CuO6 octahedra form sheets with eight-membered rings. The tetrahedral sheet composed of PO4 and ZnO3(OH) tetrahedra shows strong topological similarities to that of cavansite, gismondine, and kipushite.Diffraction data of a sample from Zdravo Vrelo, near Kreševo (Bosnia and Herzegovina) have been measured in steps of 25 up to 225 °C. Hydrogen positions and the hydrogen-bond system were determined experimentally from the structure refinements of data collected up to 125 °C. At 200 °C, the hydrogen-bonding scheme was inferred from bond-valence calculations and donor-acceptor distances. The hydrogen-bond system connects the tetrahedral sheet to the octahedral sheet and also braces the Cu sheet.At 150 °C, the H2O molecule at H2O2 was released and the Cu coordination (Cu1 and Cu2) decreased from originally six- to fivefold. Cu1 has a square planar coordination by four OH groups and an elongate distance to O3, whereas Cu2 has the Jahn-Teller characteristic elongate bond to H2O1. The unit-cell volume decreased 7% from originally 734.45(3) to 686.4(4) Å3 leading to a formula with 1 H2O pfu. The new phase observed above 150 °C is characterized by an increase of the c axis and a shortening of the b axis. The bending of T-O-T angles causes an increasing elliptical shape of the eight-membered rings in the tetrahedral and octahedral sheets. Moreover a rearrangement of the hydrogen-bond system was observed.At 225 °C, the structure degrades to an X-ray amorphous residual due to release of the last H2O molecule at H2O1. The stronger Jahn-Teller distortion of Cu1 relative to Cu2 suggests that Cu1 is fully occupied by Cu, whereas Cu2 bears significant Zn. H2O1 is the fifth ligand of Cu2. Zn at Cu2 is not favorable to adopt planar fourfold coordination. Thus, if the last water molecule is expelled the structure is destabilized.This study contributes to understanding the dehydration mechanism and thermal stability of supergene minerals characterized by Jahn-Teller distorted octahedra with mixed Cu, Zn occupancy.

Copper filtration in pediatric digital X-ray imaging: its impact on image quality and dose

The effect of copper (Cu) filtration on image quality and dose in different digital X-ray systems was investigated. Two computed radiography systems and one digital radiography detector were used. Three different polymethylmethacrylate blocks simulated the pediatric body. The effect of Cu filters of 0.1, 0.2, and 0.3 mm thickness on the entrance surface dose (ESD) and the corresponding effective doses (EDs) were measured at tube voltages of 60, 66, and 73 kV. Image quality was evaluated in a contrast-detail phantom with an automated analyzer software. Cu filters of 0.1, 0.2, and 0.3 mm thickness decreased the ESD by 25-32%, 32-39%, and 40-44%, respectively, the ranges depending on the respective tube voltages. There was no consistent decline in image quality due to increasing Cu filtration. The estimated ED of anterior-posterior (AP) chest projections was reduced by up to 23%. No relevant reduction in the ED was noted in AP radiographs of the abdomen and pelvis or in posterior-anterior radiographs of the chest. Cu filtration reduces the ESD, but generally does not reduce the effective dose. Cu filters can help protect radiosensitive superficial organs, such as the mammary glands in AP chest projections.

[How strongly does the radiation burden of diagnostic x-ray studies depend on the imaging technic?]

The radiation burden of an individual patient caused by a radiological examination depends strongly on the technical parameters, such as kV and mAs. As an inquiry among 150 swiss physicians showed, rather different irradiation techniques are used for the same examination. Depending on these irradiation techniques, the doses may vary by almost a factor of ten. These large variations in dose indicate that in some clinics or hospitals the radiographic techniques and the film processing are at fault. This fact has to be accounted for by future efforts of quality assurance in diagnostic radiology.

Effect of X-ray tube parameters, iodine concentration, and patient size on image quality in pulmonary computed tomography angiography: a chest-phantom-study

OBJECTIVES: The aim of this phantom study was to evaluate the contrast-to-noise ratio (CNR) in pulmonary computed tomography (CT)-angiography for 300 and 400 mg iodine/mL contrast media using variable x-ray tube parameters and patient sizes. We also analyzed the possible strategies of dose reduction in patients with different sizes. MATERIALS AND METHODS: The segmental pulmonary arteries were simulated by plastic tubes filled with 1:30 diluted solutions of 300 and 400 mg iodine/mL contrast media in a chest phantom mimicking thick, intermediate, and thin patients. Volume scanning was done with a CT scanner at 80, 100, 120, and 140 kVp. Tube current-time products (mAs) varied between 50 and 120% of the optimal value given by the built-in automatic dose optimization protocol. Attenuation values and CNR for both contrast media were evaluated and compared with the volume CT dose index (CTDI(vol)). Figure of merit, calculated as CNR/CTDIvol, was used to quantify image quality improvement per exposure risk to the patient. RESULTS: Attenuation of iodinated contrast media increased both with decreasing tube voltage and patient size. A CTDIvol reduction by 44% was achieved in the thin phantom with the use of 80 instead of 140 kVp without deterioration of CNR. Figure of merit correlated with kVp in the thin phantom (r = -0.897 to -0.999; P < 0.05) but not in the intermediate and thick phantoms (P = 0.09-0.71), reflecting a decreasing benefit of tube voltage reduction on image quality as the thickness of the phantom increased. Compared with the 300 mg iodine/mL concentration, the same CNR for 400 mg iodine/mL contrast medium was achieved at a lower CTDIvol by 18 to 40%, depending on phantom size and applied tube voltage. CONCLUSIONS: Low kVp protocols for pulmonary embolism are potentially advantageous especially in thin and, to a lesser extent, in intermediate patients. Thin patients profit from low voltage protocols preserving a good CNR at a lower exposure. The use of 80 kVp in obese patients may be problematic because of the limitation of the tube current available, reduced CNR, and high skin dose. The high CNR of the 400 mg iodine/mL contrast medium together with lower tube energy and/or current can be used for exposure reduction.

Finite element 3D reconstruction of the pulmonary acinus imaged by synchrotron X-ray tomography

The alveolated structure of the pulmonary acinus plays a vital role in gas exchange function. Three-dimensional (3D) analysis of the parenchymal region is fundamental to understanding this structure-function relationship, but only a limited number of attempts have been conducted in the past because of technical limitations. In this study, we developed a new image processing methodology based on finite element (FE) analysis for accurate 3D structural reconstruction of the gas exchange regions of the lung. Stereologically well characterized rat lung samples (Pediatr Res 53: 72-80, 2003) were imaged using high-resolution synchrotron radiation-based X-ray tomographic microscopy. A stack of 1,024 images (each slice: 1024 x 1024 pixels) with resolution of 1.4 mum(3) per voxel were generated. For the development of FE algorithm, regions of interest (ROI), containing approximately 7.5 million voxels, were further extracted as a working subunit. 3D FEs were created overlaying the voxel map using a grid-based hexahedral algorithm. A proper threshold value for appropriate segmentation was iteratively determined to match the calculated volume density of tissue to the stereologically determined value (Pediatr Res 53: 72-80, 2003). The resulting 3D FEs are ready to be used for 3D structural analysis as well as for subsequent FE computational analyses like fluid dynamics and skeletonization.

High-temperature induced dehydration, phase transition and exsolution in amicite: A single-crystal X-ray study

Temperature dependent single-crystal X-ray data were collected on amicite K4Na4(Al8Si8O32)·11H2O from Kola Peninsula (Russia) in steps of 25 °C from room temperature to 175 °C and of 50 °C up to 425 °C. At room temperature amicite has space group I2 with a = 10.2112(1), b = 10.4154(1), c = 9.8802(1) Å, β = 88.458(1)°, V = 1050.416(18) Å3. Its crystal structure is based on a Si–Al ordered tetrahedral framework of the GIS type with two systems of eight-membered channels running along the a and c axes. Extraframework K and Na cations are ordered at two fully occupied sites. Above 75 °C amicite was found to partly dehydrate into two separate but coherently intergrown phases, both of space group I2/a, one K-rich ∼K8(Al8Si8O32) ·4H2O (at 75 °C: a = 10.038(2), b = 9.6805(19), c = 9.843(2) Å, β = 89.93(3)°, V = 956.5(3) Å3) and the other Na-rich ∼Na8(Al8Si8O32)·2H2O (at 75 °C: a = 9.759(2), b = 8.9078(18), c = 9.5270(19) Å, β = 89.98(3)°, V = 828.2(3) Å3). Upon further heating above 75 °C the Na- and K-phases lost remaining H2O with only minor influence on the framework structure and became anhydrous at 175 °C and 375 °C, respectively. The two anhydrous phases persisted up to 425 °C. Backscattered electron images of a heated crystal displayed lamellar intergrowth of the K- and Na-rich phases. Exposed to ambient humid conditions K- and Na-rich phases rehydrated and conjoined to the original one phase I2 structure.

In situ dehydration behavior of zeolite-like cavansite: A single-crystal X-ray study

To track dehydration behavior of cavansite, Ca(VO)(Si4O10)·4H2O space group Pnma, a = 9.6329(2), b = 13.6606(2), c = 9.7949(2) Å, V = 1288.92(4) Å3 single-crystal X-ray diffraction data on a crystal from Wagholi quarry, Poona district (India) were collected up to 400 °C in steps of 25 °C up to 250 °C and in steps of 50 °C between 250 and 400 °C. The structure of cavansite is characterized by layers of silicate tetrahedra connected by V4+O5 square pyramids. This way a porous framework structure is formed with Ca and H2O as extraframework occupants. At room temperature, the hydrogen bond system was analyzed. Ca is eightfold coordinated by four bonds to O of the framework structure and four bonds to H2O molecules. H2O linked to Ca is hydrogen bonded to the framework and also to adjacent H2O molecules. The dehydration in cavansite proceeds in four steps.At 75 °C, H2O at O9 was completely expelled leading to 3 H2O pfu with only minor impact on framework distortion and contraction V = 1282.73(3) Å3. The Ca coordination declined from originally eightfold to sevenfold and H2O at O7 displayed positional disorder.At 175 °C, the split O7 sites approached the former O9 position. In addition, the sum of the three split positions O7, O7a, and O7b decreased to 50% occupancy yielding 2 H2O pfu accompanied by a strong decrease in volume V = 1206.89(8) Å3. The Ca coordination was further reduced from sevenfold to sixfold.At 350 °C, H2O at O8 was released leading to a formula with 1 H2O pfu causing additional structural contraction (V = 1156(11) Å3). At this temperature, Ca adopted fivefold coordination and O7 rearranged to disordered positions closer to the original O9 H2O site.At 400 °C, cavansite lost crystallinity but the VO2+ characteristic blue color was preserved. Stepwise removal of water is discussed on the basis of literature data reporting differential thermal analyses, differential thermo-gravimetry experiments and temperature dependent IR spectra in the range of OH stretching vibrations.

In-situ X-ray micro-diffraction studies of heterogeneous interfaces between cementitious materials and geological formations

In the present study the challenge of analyzing complex micro X-ray diffraction (microXRD) patterns from cement–clay interfaces has been addressed. In order to extract the maximum information concerning both the spatial distribution and the crystal structure type associated with each of the many diffracting grains in heterogeneous, polycrystalline samples, an approach has been developed in which microXRD was applied to thin sections which were rotated in the X-ray beam. The data analysis, performed on microXRD patterns collected from a filled vein of a cement–clay interface from the natural analogue in Maqarin (Jordan), and a sample from a two-year-old altered interface between cement and argillaceous rock, demonstrate the potential of this method.

Quantitative 3D strain analysis in analogue experiments: Integration of X-ray computed tomography and digital volume correlation techniques

The combination of scaled analogue experiments, material mechanics, X-ray computed tomography (XRCT) and Digital Volume Correlation techniques (DVC) is a powerful new tool not only to examine the 3 dimensional structure and kinematic evolution of complex deformation structures in scaled analogue experiments, but also to fully quantify their spatial strain distribution and complete strain history. Digital image correlation (DIC) is an important advance in quantitative physical modelling and helps to understand non-linear deformation processes. Optical non-intrusive (DIC) techniques enable the quantification of localised and distributed deformation in analogue experiments based either on images taken through transparent sidewalls (2D DIC) or on surface views (3D DIC). X-ray computed tomography (XRCT) analysis permits the non-destructive visualisation of the internal structure and kinematic evolution of scaled analogue experiments simulating tectonic evolution of complex geological structures. The combination of XRCT sectional image data of analogue experiments with 2D DIC only allows quantification of 2D displacement and strain components in section direction. This completely omits the potential of CT experiments for full 3D strain analysis of complex, non-cylindrical deformation structures. In this study, we apply digital volume correlation (DVC) techniques on XRCT scan data of “solid” analogue experiments to fully quantify the internal displacement and strain in 3 dimensions over time. Our first results indicate that the application of DVC techniques on XRCT volume data can successfully be used to quantify the 3D spatial and temporal strain patterns inside analogue experiments. We demonstrate the potential of combining DVC techniques and XRCT volume imaging for 3D strain analysis of a contractional experiment simulating the development of a non-cylindrical pop-up structure. Furthermore, we discuss various options for optimisation of granular materials, pattern generation, and data acquisition for increased resolution and accuracy of the strain results. Three-dimensional strain analysis of analogue models is of particular interest for geological and seismic interpretations of complex, non-cylindrical geological structures. The volume strain data enable the analysis of the large-scale and small-scale strain history of geological structures.