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Journal of Applied Crystallography Jun 2022A description is given of the program . This program is used for visualizing powder diffraction data and models published in powder CIF format (pdCIF). In particular,...
A description is given of the program . This program is used for visualizing powder diffraction data and models published in powder CIF format (pdCIF). In particular, support for the visualization of multi-pattern data sets, such as diffraction experiments, is provided by means of stack and surface plots. is written in Python 3 and can run wherever a compatible runtime is available. macros for the production of pdCIF files are also presented.
PubMed: 35719308
DOI: 10.1107/S1600576722003478 -
Journal of Visualized Experiments : JoVE Jan 2017In this report we describe detailed procedures for carrying out single crystal X-ray diffraction experiments with a diamond anvil cell (DAC) at the GSECARS 13-BM-C...
In this report we describe detailed procedures for carrying out single crystal X-ray diffraction experiments with a diamond anvil cell (DAC) at the GSECARS 13-BM-C beamline at the Advanced Photon Source. The DAC program at 13-BM-C is part of the Partnership for Extreme Xtallography (PX^2) project. BX-90 type DACs with conical-type diamond anvils and backing plates are recommended for these experiments. The sample chamber should be loaded with noble gas to maintain a hydrostatic pressure environment. The sample is aligned to the rotation center of the diffraction goniometer. The MARCCD area detector is calibrated with a powder diffraction pattern from LaB6. The sample diffraction peaks are analyzed with the ATREX software program, and are then indexed with the RSV software program. RSV is used to refine the UB matrix of the single crystal, and with this information and the peak prediction function, more diffraction peaks can be located. Representative single crystal diffraction data from an omphacite (Ca0.51Na0.48)(Mg0.44Al0.44Fe0.14Fe0.02)Si2O6 sample were collected. Analysis of the data gave a monoclinic lattice with P2/n space group at 0.35 GPa, and the lattice parameters were found to be: a = 9.496 ±0.006 Å, b = 8.761 ±0.004 Å, c = 5.248 ±0.001 Å, β = 105.06 ±0.03º, α = γ = 90º.
Topics: Crystallography, X-Ray; Diamond; Powder Diffraction; Pressure; Synchrotrons
PubMed: 28117811
DOI: 10.3791/54660 -
Biomolecules Aug 2017Human insulin (HI) is a well-characterized natural hormone which regulates glycose levels into the blood-stream and is widely used for diabetes treatment. Numerous... (Review)
Review
Human insulin (HI) is a well-characterized natural hormone which regulates glycose levels into the blood-stream and is widely used for diabetes treatment. Numerous studies have manifested that despite significant efforts devoted to structural characterization of this molecule and its complexes with organic compounds (ligands), there is still a rich diagram of phase transitions and novel crystalline forms to be discovered. Towards the improvement of drug delivery, identification of new insulin polymorphs from polycrystalline samples, simulating the commercially available drugs, is feasible today via macromolecular X-ray powder diffraction (XRPD). This approach has been developed, and is considered as a respectable method, which can be employed in biosciences for various purposes, such as observing phase transitions and characterizing bulk pharmaceuticals. An overview of the structural studies on human insulin complexes performed over the past decade employing both synchrotron and laboratory sources for XRPD measurements, is reported herein. This review aims to assemble all of the recent advances in the diabetes treatment field in terms of drug formulation, verifying in parallel the efficiency and applicability of protein XRPD for quick and accurate preliminary structural characterization in the large scale.
Topics: Diabetes Mellitus; Humans; Hypoglycemic Agents; Insulin; Phenols; Powder Diffraction; Structure-Activity Relationship; X-Ray Diffraction
PubMed: 28829407
DOI: 10.3390/biom7030063 -
Crystal Growth & Design Apr 2023The materials property of ferroelectricity is intimately linked with symmetry-changing phase transitions. Characterizing such transitions is therefore essential for...
The materials property of ferroelectricity is intimately linked with symmetry-changing phase transitions. Characterizing such transitions is therefore essential for understanding molecular ferroelectrics. In this paper, we explore the temperature and thermal history dependence of polymorphic phase transitions in the multiaxial molecular ferroelectric 18-crown-6 oxonium tetrachloro-gallium(III). We have solved the structures of two previously suggested polymorphs (D and Y) from high-temperature powder diffraction data. We also report the structure of a new polymorph (X) using low-temperature powder diffraction data and identify a fifth (W) that can form on cooling. These polymorphs can be related using two distinct group-subgroup trees. Structure types A-C observed in this and related compounds can be derived from high-temperature polymorph D by group-subgroup relationships. The X and Y polymorphs can be described as child structures of a hypothetical polymorph Z using a molecular rotational distortion mode description. The ferroelectric properties of the various polymorphs can be rationalized based on our structural findings.
PubMed: 37038399
DOI: 10.1021/acs.cgd.3c00017 -
Physics and Chemistry of Minerals 2017Starting from a synthetic sample with composition Al(SO)·16.6HO, the high-temperature- and moisture-dependent behavior of alunogen has been unraveled by TGA...
Starting from a synthetic sample with composition Al(SO)·16.6HO, the high-temperature- and moisture-dependent behavior of alunogen has been unraveled by TGA measurements, in situ powder X-ray diffraction as well as by gravimetric moisture sorption/desorption studies. Heating experiments using the different techniques show that alunogen undergoes a first dehydration process already starting at temperatures slightly above 40 °C. The crystalline product of the temperature-induced dehydration corresponds to the synthetic equivalent of meta-alunogen and has the following chemical composition: Al(SO)·13.8HO or Al(SO)(HO)·1.8HO. At 90 °C a further reaction can be monitored resulting in the formation of an X-ray amorphous material. The sequence of "amorphous humps" in the patterns persists up to 250 °C, where a re-crystallization process is indicated by a sudden appearance of a larger number of sharp Bragg peaks. Phase analysis confirmed this compound to be anhydrous Al(SO). Furthermore, meta-alunogen can be also obtained from alunogen at room temperature when stored at relative humidities (RH) lower than 20 %. The transformation is reversible, however, water sorption of meta-alunogen to alunogen and the corresponding desorption reaction show considerable hysteresis. For RH values above 80 %, deliquescence of the material was observed. Structural investigations on meta-alunogen were performed using a sample that has been stored at dry conditions (0 % RH) over phosphorus pentoxide. Powder diffraction data were acquired on an in-house high-resolution diffractometer in transmission mode using a sealed glass capillary as sample holder. Indexing resulted in a triclinic unit cell with the following lattice parameters: = 14.353(6) Å, = 12.490(6) Å, = 6.092(3) Å, = 92.656(1)°, = 96.654(1)°, = 100.831(1)°, = 1062.8(8) Å and = 2. These data correct earlier findings suggesting an orthorhombic cell. Ab-initio structure solution in space group [Formula: see text], using simulated annealing, provided a chemically meaningful structure model. The asymmetric unit of meta-alunogen contains three symmetry independent SO-tetrahedra and two Al(HO) octahedra. The polyhedra are isolated, however, linkage between them is provided by Coulomb interactions and hydrogen bonding. In addition to the water molecules which directly belong to the coordination environment of the aluminum cations there are two additional zeolitic water sites (Ow1 and Ow2). If both positions are fully occupied meta-alunogen corresponds to a 14-hydrate. Structural similarities and differences between the previously unknown structure of meta-alunogen and alunogen are discussed in detail. Since hydrous aluminum sulfates have been postulated to occur in Martian soils, our results may help identifying meta-alunogen by X-ray diffraction not only on the surface of the Earth but also using the Curiosity Rover's ChemMin instrument.
PubMed: 28239226
DOI: 10.1007/s00269-016-0840-7 -
Acta Crystallographica. Section D,... May 2023The polymorphism of human insulin upon pH variation was characterized via X-ray powder diffraction, employing a crystallization protocol previously established for...
The polymorphism of human insulin upon pH variation was characterized via X-ray powder diffraction, employing a crystallization protocol previously established for co-crystallization with phenolic derivatives. Two distinct rhombohedral (R3) polymorphs and one cubic (I23) polymorph were identified with increasing pH, corresponding to the T, TR and T conformations of insulin, respectively. The structure of the cubic T polymorph was determined via multi-profile stereochemically restrained Rietveld refinement at 2.7 Å resolution. This constitutes the first cubic insulin structure to be determined from crystals grown in the presence of zinc ions, although no zinc binding was observed. The differences of the polycrystalline variant from other cubic insulin structures, as well as the nature of the pH-driven phase transitions, are discussed in detail.
Topics: Humans; Insulin; X-Ray Diffraction; Insulin, Regular, Human; Phenols; Crystallization
PubMed: 37039669
DOI: 10.1107/S2059798323001328 -
Journal of Applied Crystallography Dec 2020Lahey-Rudolph and co-workers [ (2020), , 1169-1180] have reported a rapid and sensitive method to screen for crystals - a welcome addition to the structural biology...
Lahey-Rudolph and co-workers [ (2020), , 1169-1180] have reported a rapid and sensitive method to screen for crystals - a welcome addition to the structural biology toolbox.
PubMed: 33304219
DOI: 10.1107/S1600576720014971 -
Journal of Applied Crystallography Dec 2015This paper introduces a two-dimensional extension of the well established Rietveld refinement method for modeling neutron time-of-flight powder diffraction data. The...
This paper introduces a two-dimensional extension of the well established Rietveld refinement method for modeling neutron time-of-flight powder diffraction data. The novel approach takes into account the variation of two parameters, diffraction angle 2θ and wavelength λ, to optimally adapt to the varying resolution function in diffraction experiments. By doing so, the refinement against angular- and wavelength-dispersive data gets rid of common data-reduction steps and also avoids the loss of high-resolution information typically introduced by integration. In a case study using a numerically simulated diffraction pattern of RhFeN taking into account the layout of the future POWTEX instrument, the profile function as parameterized in 2θ and λ is extracted. As a proof-of-concept, the resulting instrument parameterization is then utilized to perform a typical refinement of the angular- and wavelength-dispersive diffraction pattern of CuNCN, yielding excellent residuals within feasible computational efforts. Another proof-of-concept is carried out by applying the same approach to a real neutron diffraction data set of CuNCN obtained from the POWGEN instrument at the Spallation Neutron Source in Oak Ridge. The paper highlights the general importance of the novel approach for data analysis at neutron time-of-flight diffractometers and its possible inclusion within existing Rietveld software packages.
PubMed: 26664340
DOI: 10.1107/S1600576715016520 -
Journal of Applied Crystallography Aug 2022Transmission electron microscopy is a powerful experimental tool, very effective for the complete characterization of nanocrystalline materials by employing a...
Transmission electron microscopy is a powerful experimental tool, very effective for the complete characterization of nanocrystalline materials by employing a combination of imaging, spectroscopy and diffraction techniques. Electron powder diffraction (EPD) pattern fingerprinting in association with chemical information from spectroscopy can be used to deduce the identity of the crystalline phases. Furthermore, EPD has similar potential to X-ray powder diffraction (XRPD) for extracting additional information regarding material specimens, such as microstructural features and defect structures. The aim of this paper is to extend a full-pattern fitting procedure, broadly used for analysing XRPD patterns, to EPD. The interest of this approach is twofold: in the first place, the relatively short times involved with data acquisition allow one to speed up the characterization procedures. This is a particularly interesting aspect in the case of metastable structures or kinetics studies. Moreover, the reduced sampling volumes involved with electron diffraction analyses can better reveal surface alteration layers in the analysed specimen which might be completely overlooked by conventional bulk techniques. The first step forward to have an effective application of the proposed methodology concerns establishing a reliable calibration protocol to take into correct account the instrumental effects and thus separate them from those determined by the structure, microstructure and texture of the analysed samples. In this paper, the methodology for determining the instrumental broadening of the diffraction lines is demonstrated through a full quantitative analysis based on the Rietveld refinement of the EPD. In this regard, a CeO nanopowder reference specimen has been used. The results provide indications also on the specific features that a good calibration standard should have.
PubMed: 35974734
DOI: 10.1107/S1600576722006367 -
Acta Crystallographica Section B,... Apr 2022A method of ab initio crystal structure determination from powder diffraction data for organic and metal-organic compounds, which does not require prior indexing of the...
A method of ab initio crystal structure determination from powder diffraction data for organic and metal-organic compounds, which does not require prior indexing of the powder pattern, has been developed. Only a reasonable molecular geometry is required, needing knowledge of neither unit-cell parameters nor space group. The structures are solved from scratch by a global fit to the powder data using the new program FIDEL-GO (`FIt with DEviating Lattice parameters - Global Optimization'). FIDEL-GO uses a similarity measure based on cross-correlation functions, which allows the comparison of simulated and experimental powder data even if the unit-cell parameters deviate strongly. The optimization starts from large sets of random structures in various space groups. The unit-cell parameters, molecular position and orientation, and selected internal degrees of freedom are fitted simultaneously to the powder pattern. The optimization proceeds in an elaborate multi-step procedure with built-in clustering of duplicate structures and iterative adaptation of parameter ranges. The best structures are selected for an automatic Rietveld refinement. Finally, a user-controlled Rietveld refinement is performed. The procedure aims for the analysis of a wide range of `problematic' powder patterns, in particular powders of low crystallinity. The method can also be used for the clustering and screening of a large number of possible structure candidates and other application scenarios. Examples are presented for structure determination from unindexed powder data of the previously unknown structures of the nanocrystalline phases of 4,11-difluoro-, 2,9-dichloro- and 2,9-dichloro-6,13-dihydro-quinacridone, which were solved from powder patterns with 14-20 peaks only, and of the coordination polymer dichloro-bis(pyridine-N)copper(II).
Topics: Copper; Polymers; Powder Diffraction; Powders
PubMed: 35411858
DOI: 10.1107/S2052520622001500