Synthetic, EPR spectroscopic, magnetic and X-ray crystallographic structural studies on copper(II) complexes of the tridentate N2S donor ligand formed from 6-methyl-2-formylpyridine and S-methyldithiocarbazate (Hmpsme)

New copper(II) complexes of general empirical formula, Cu(mpsme)X center dot xCH(3)COCH(3) (mpsme = anionic form of the 6-methyl-2-formylpyridine Schiff base of S-methyldithiocarbazate; X = Cl, N-3, NCS, NO3; x = 0, 0.5) have been synthesized and characterized by IR, electronic, EPR and susceptibility measurements. Room temperature mu(eff) values for the complexes are in the range 1.75-2.1 mu(beta) typical of uncoupled or weakly coupled Cu(II) centres. The EPR spectra of the [Cu(mpsme)X] (X = Cl, N-3, NO3, NCS) complexes reveal a tetragonally distorted coordination sphere around the mononuclear Cu(II) centre. We have exploited second derivative EPR spectra in conjunction with Fourier filtering (sine bell and Hamming functions) to extract all of the nitrogen hyperfine coupling matrices. While the X-ray crystallography of [Cu(mpsme)NCS] reveals a linear polymer in which the thiocyanate anion bridges the two copper(II) ions, the EPR spectra in solution are typical of a magnetically isolated monomeric Cu(II) centres indicating dissociation of the polymeric chain in solution. The structures of the free ligand, Hmpsme and the {[Cu(mpsme)NO3] center dot 0.5CH(3)COCH(3)}(2) and [Cu(mpsme)NCS](n) complexes have been determined by X-ray diffraction. The {[Cu(mpsme)NO3]0.5CH(3)COCH(3)}(2) complex is a centrosymmetric dimer in which each copper atom adopts a five-coordinate distorted square-pyramidal geometry with an N2OS2 coordination environment, the Schiff base coordinating as a uninegatively charged tridentate ligand chelating through the pyridine and azomethine nitrogen atoms and the thiolate, an oxygen atom of a unidentate nitrato ligand and a bridging sulfur atom from the second ligand completing the coordination sphere. The [Cu(mpsme)(NCS)](n) complex has a novel staircase-like one dimensional polymeric structure in which the NCS- ligands bridge two adjacent copper(II) ions asymmetrically in an end-to-end fashion providing its nitrogen atom to one copper and the sulfur atom to the other. (c) 2005 Elsevier B.V. All rights reserved.

Structural properties of a family of hydrogen-bonded co-crystals formed between gemfibrozil and hydroxy derivatives of t-butylamine, determined directly from powder X-ray diffraction data

We report the formation and structural properties of co-crystals containing gemfibrozil and hydroxy derivatives of t-butylamine H2NC(CH3)3-n(CH2OH)n, with n=0, 1, 2 and 3. In each case, a 1:1 co-crystal is formed, with transfer of a proton from the carboxylic acid group of gemfibrozil to the amino group of the t-butylamine derivative. All of the co-crystal materials prepared are polycrystalline powders, and do not contain single crystals of suitable size and/or quality for single crystal X-ray diffraction studies. Structure determination of these materials has been carried out directly from powder X-ray diffraction data, using the direct-space Genetic Algorithm technique for structure solution followed by Rietveld refinement. The structural chemistry of this series of co-crystal materials reveals well-defined structural trends within the first three members of the family (n=0, 1, 2), but significantly contrasting structural properties for the member with n=3. © 2007 Elsevier Inc. All rights reserved.

Deformation microstructure under nanoindentations in Cu using 3D x-ray structural microscopy

We have used a recently developed x-ray structural microscopy technique to make nondestructive, submicron-resolution measurements of the deformation microstructure below a 100mN maximum load Berkovich nanoindent in single crystal Cu. Direct observations of plastic deformation under the indent were obtained using a ~0.5 µm polychromatic microbeam and diffracted beam depth profiling to make micron-resolution spatially-resolved x-ray Laue diffraction measurements. The local lattice rotations underneath the nanoindent were found to be heterogeneous in nature as revealed by geometrically necessary dislocation (GND) densities determined for positions along lines beneath a flat indent face and under the sharp Berkovich indent blade edges. Measurements of the local rotation-axes and misorientation-angles along these lines are discussed in terms of crystallographic slip systems.

Implementation of X-ray diffraction in the measurement of residual thermal strains

Microelectronic systems are multi-material, multi-layer structures, fabricated and exposed to environmental stresses over a wide range of temperatures. Thermal and residual stresses created by thermal mismatches in films and interconnections are a major cause of failure in microelectronic devices. Due to new device materials, increasing die size and the introduction of new materials for enhanced thermal management, differences in thermal expansions of various packaging materials have become exceedingly important and can no longer be neglected. X-ray diffraction is an analytical method using a monochromatic characteristic X-ray beam to characterize the crystal structure of various materials, by measuring the distances between planes in atomic crystalline lattice structures. As a material is strained, this interplanar spacing is correspondingly altered, and this microscopic strain is used to determine the macroscopic strain. This thesis investigates and describes the theory and implementation of X-ray diffraction in the measurement of residual thermal strains. The design of a computer controlled stress attachment stage fully compatible with an Anton Paar heat stage will be detailed. The stress determined by the diffraction method will be compared with bimetallic strip theory and finite element models.

A Staggered Decameric Assembly of Human C-Reactive Protein Stabilized by Zinc Ions Revealed by X-ray Crystallography

International audience

X-Ray powder diffraction laboratory @ University of Málaga (UMA)

X-Ray Powder Diffraction (XRPD) laboratory is a facility placed at Servicios Centrales de apoyo a la Investigación (SCAI) at University of Malaga (UMA) http://www.scai.uma.es/. This facility has three XRPD diffractometers and a diffractometer to measure high-resolution thin-films. X´Pert PRO MPD from PANalytical. This is a bragg-brentano (theta/2theta) with reflection geometry diffractometer which allows to obtain high resolution XRPD data with strictly monochromatic CuKα1 radiation (λ=1.54059Å) [Ge(111) primary monochromator] and an automatic sample charger. Moreover, it has parallel monochromatic CuKα1 radiation (λ=1.54059Å) with an hybrid Ge(220) monochromator for capillary and multiproposal (bulk samples up to 1 Kg) sample holders. The HTK1200N chamber from Anton Paar allows collecting high resolution high temperature patterns. EMPYREAN from PANalytical. This diffractometer works in reflection and transmission geometries with theta/theta goniometer, using CuKα1,2 radiation (λ=1.5418Å), a focusing X-ray mirror and a ultra-fast PIXCEL 3D detector with 1D and 2D collection data modes (microstructural and preferred orientation analysis). Moreover, the TTK450N chamber allows low temperature and up to 450ºC studies. A D8 ADVANCE (BRUKER) was installed in April 2014. It is the first diffractometer in Europe equipped with a Johansson Ge(111) primary monochromator, which gives a strictly monochromatic Mo radiation (λ=0.7093 Å) [1]. It works in transmission mode (with a sample charger) with this high resolution configuration. XRPD data suitable for PDF (Pair Distribution Function) analysis can be collected with a capillary sample holder, due to the high energy and high resolution capabilities of this diffractometer. Moreover, it has a humidity chamber MHC-trans from Anton Paar working on transmission mode with MoKα1 (measurements can be collected at 5 to 95% of relative humidity (from 20 to 80 ºC) and up to 150ºC [2]). Furthermore, this diffractometer also has a reaction chamber XRK900 from Anton Paar (which uses CuKα1,2 radiation in reflection mode), which allows data collection from room temperature to 900ºC with up to 10 bar of different gases. Finally, a D8 DISVOVER A25 from BRUKER was installed on December 2014. It has a five axis Euler cradler and optics devices suitable for high resolution thin film data collection collected in in-plane and out-of-plane modes. To sum up, high-resolution thin films, microstructural, rocking-curve, Small Angle X-ray Scattering (SAXS), Grazing incident SAXS (GISAXS), Ultra Grazing incident diffraction (Ultra-GID) and microdiffraction measurements can be performed with the appropriated optics and sample holders. [1] L. León-Reina, M. García-Maté, G. Álvarez-Pinazo, I. Santacruz, O. Vallcorba, A.G. De la Torre, M.A.G. Aranda “Accuracy in Rietveld quantitative phase analysis: a comparative study of strictly monochromatic Mo and Cu radiations” J. Appl. Crystallogr. 2016, 49, 722-735. [2] J. Aríñez-Soriano, J. Albalad, C. Vila-Parrondo, J. Pérez-Carvajal, S. Rodríguez-Hermida, A. Cabeza, F. Busqué, J. Juanhuix, I. Imaz, Daniel Maspoch “Single-crystal and humidity-controlled powder diffraction study of the breathing effect in a metal-organic framework upon water adsorption/desorption” Chem. Commun., 2016, DOI: 10.1039/C6CC02908F.

Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography

Archaeal replicative DNA polymerase D (PolD) constitute an atypical class of DNA polymerases made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2), both with unknown structures. We have determined the crystal structures of Pyrococcus abyssi DP1 and DP2 at 2.5 and 2.2 angstrom resolution, respectively, revealing a catalytic core strikingly different from all other known DNA polymerases (DNAPs). Rather, the PolD DP2 catalytic core has the same 'double-psi beta-barrel' architecture seen in the RNA polymerase (RNAP) superfamily, which includes multi-subunit transcriptases of all domains of life, homodimeric RNA-silencing pathway RNAPs and atypical viral RNAPs. This finding bridges together, in non-viral world, DNA transcription and DNA replication within the same protein superfamily. This study documents further the complex evolutionary history of the DNA replication apparatus in different domains of life and proposes a classification of all extant DNAPs.

Applications of synchrotron x-ray powder diffraction in hydrated cements: high-resolution and high-pressure studies

The main aim of this study is to apply synchrotron radiation techniques for the study of hydrated cement pastes. In particular, the tetracalcium aluminoferrite phase, C4AF in cement nomenclature, is the major iron-containing phase in Ordinary Portland Cement (OPC) and in iron rich belite calcium sulfoaluminate cements. In a first study, the hydration mechanism of pure tetracalcium aluminoferrite phase with water-to-solid ratio of 1.0 has been investigated by HR-SXRPD (high resolution synchrotron X-ray powder diffraction). C4AF in the presence of water hydrates to form mainly an iron-containing hydrogarnet-type (katoite) phase, C3A0.84F0.16H6, as single crystalline phase. Its crystal structure and stoichiometry were determined by the Rietveld method and the final disagreement factors were RWP=8.1% and RF=4.8% [1]. As the iron content in the product is lower than that in C4AF, it is assumed that part of the iron also goes to an amorphous iron rich gel, like the hydrated alumina-type gel, as hydration proceeds. Further results from the high-resolution study will be discussed. In a second study, the behavior of pure and iron-containing katoites (C3AH6 and C3A0.84F0.16H6) under pressure have been analyzed by SXRPD using a diamond anvil cell (DAC) and then their bulk moduli were determined. The role of the pressure transmitting medium (PTM) has also been studied. In this case, silicone oil as well as methanol/ethanol mixtures have been used as PTM. Some “new peaks” were detected in the pattern for C3A0.84F0.16H6 as pressure increases, when using ethanol/methanol as PTM. These new peaks were still present at ambient pressure after releasing the applied pressure. They may correspond to crystalline nordstrandite or doyleite from the crystallization of amorphous aluminium hydroxide. The results from the high-pressure study will also be discussed.

Ethnic differences in the BMI-%BF relationships between young Japanese and Australian-Caucasian males living in Australia using dual-energy X-ray absorptiometry

The Body Mass Index (BMI) has been used worldwide as an indicator of fatness. However, the universal cut-off points by the World Health Organisation (WHO) classification may not be appropriate for every ethnic group when consider the relationship with their actual total body fatness(%BF). The application of population-specific classifications to assess BMI may be more relevant to public health. Ethnic differences in the BMI%BF relationship between 45 Japanese and 42 Australian-Caucasian males were assessed using whole body dual-energy X-ray absorptiometry (DXA) scan and anthropometry using a standard protocol. Japanese males had significantly (p<0.05) greater %BF at given BMI values than Australian males. When this is taken into account the newly proposed Asia-Pacific BMI classification of BMI 23 as overweight and 25 as obese may better assess the level of obesity that is associated increased health risks for this population. To clarify the current findings, further studies that compare the relationships across other Japanese populations are recommended.

X-ray your data with Rasch

By using the Rasch model, much detailed diagnostic information is available to developers of survey and assessment instruments and to the researchers who use them. We outline an approach to the analysis of data obtained from the administration of survey instruments that can enable researchers to recognise and diagnose difficulties with those instruments and then to suggest remedial actions that can improve the measurement properties of the scales included in questionnaires. We illustrate the approach using examples drawn from recent research and demonstrate how the approach can be used to generate figures that make the results of Rasch analyses accessible to non-specialists.

3-D reconstruction of an ancient Egyptian mummy using X-ray computer tomography

Computer tomography has been used to image and reconstruct in 3-D an Egyptian mummy from the collection of the British Museum. This study of Tjentmutengebtiu, a priestess from the 22nd dynasty (945-715 BC) revealed invaluable information of a scientific, Egyptological and palaeopathological nature without mutilation and destruction of the painted cartonnage case or linen wrappings. Precise details on the removal of the brain through the nasal cavity and the viscera from the abdominal cavity were obtained. The nature and composition of the false eyes were investigated. The detailed analysis of the teeth provided a much closer approximation of age at death. The identification of materials used for the various amulets including that of the figures placed in the viscera was graphically demonstrated using this technique.

X-ray computed tomography

X-ray computed tomography (CT) is a medical imaging technique that produces images of trans-axial planes through the human body. When compared with a conventional radiograph, which is an image of many planes superimposed on each other, a CT image exhibits significantly improved contrast although this is at the expense of reduced spatial resolution.----- A CT image is reconstructed mathematically from a large number of one dimensional projections of the chosen plane. These projections are acquired electronically using a linear array of solid-state detectors and an x ray source that rotates around the patient.----- X-ray computed tomography is used routinely in radiological examinations. It has also be found to be useful in special applications such as radiotherapy treatment planning and three-dimensional imaging for surgical planning.

Smectite flocculation structure modified by AI13 macromolecules; as revealed by the Transmission X-ray Microscopy (TXM)

The aggregate structure which occurs in aqueous smectitic suspensions is responsible for poor water clarification, difficulties in sludge dewatering and the unusual rheological behaviour of smectite rich soils. These macroscopic properties are dictated by the 3-D structural arrangement of smectite finest fraction within flocculated aggregates. Here, we report results from a relatively new technique, Transmission X-ray Microscopy (TXM), which makes it possible to investigate the internal structure and 3-D tomographic reconstruction of the smectite clay aggregates modified by Al13 keggin macro-molecule [Al13(O)4(OH)24(H2O)12 ]7+. Three different treatment methods were shown resulted in three different micro-structural environments of the resulting flocculation.