scholarly journals Slow cooling of protein crystals

2009 ◽  
Vol 42 (5) ◽  
pp. 944-952 ◽  
Author(s):  
Matthew Warkentin ◽  
Robert E. Thorne
Keyword(s):  
Ice Nucleation ◽  
Glycerol Solution ◽  
X Ray Diffraction ◽  
Slow Cooling ◽  
Sodium Potassium ◽  
X Ray ◽  
Structure And Dynamics ◽  
Potassium Tartrate ◽  
Flash Cooling ◽  
Diffraction Patterns

Cryoprotectant-free thaumatin crystals have been cooled from 300 to 100 K at a rate of 0.1 K s−1– 103–104times slower than in conventional flash cooling – while continuously collecting X-ray diffraction data, so as to follow the evolution of protein lattice and solvent properties during cooling. Diffraction patterns show no evidence of crystalline ice at any temperature. This indicates that the lattice of protein molecules is itself an excellent cryoprotectant, and with sodium potassium tartrate incorporated from the 1.5 Mmother liquor ice nucleation rates are at least as low as in a 70% glycerol solution. Crystal quality during slow cooling remains high, with an average mosaicity at 100 K of 0.2°. Most of the mosaicity increase occurs above ∼200 K, where the solvent is still liquid, and is concurrent with an anisotropic contraction of the unit cell. Near 180 K a crossover to solid-like solvent behavior occurs, and on further cooling there is no additional degradation of crystal order. The variation ofBfactor with temperature shows clear evidence of a protein dynamical transition near 210 K, and at lower temperatures the slope dB/dTis a factor of 3–6 smaller than has been reported for any other protein. These results establish the feasibility of fully temperature controlled studies of protein structure and dynamics between 300 and 100 K.

Structural and phase equilibria studies in the system Pt-Fe-Cu and the occurrence of tulameenite (Pt2FeCu)

1985 ◽  
Vol 49 (353) ◽  
pp. 547-554 ◽  
Author(s):  
M. Shahmiri ◽  
S. Murphy ◽  
D. J. Vaughan
Keyword(s):  
Crystal Structure ◽  
Solid Solution ◽  
Critical Temperature ◽  
Grain Boundary ◽  
Phase Region ◽  
X Ray Diffraction ◽  
Two Phase ◽  
Slow Cooling ◽  
X Ray ◽  
Diffraction Patterns

AbstractThe crystal structure and compositional limits of the ternary compound Pt2FeCu (tulameenite), formed either by quenching from above the critical temperature of 1178°C or by slow cooling, have been investigated using X-ray diffraction, transmission electron microscopy, differential thermal analysis and electron probe microanalysis.The crystal structure of Pt2FeCu, established using electron density maps constructed from the measured and calculated intensities of X-ray diffraction patterns of powdered specimens, has the (000) and (½½0) lattice sites occupied by Pt atoms and the (½0½) and (0½½) sites occupied by either Cu or Fe atoms in a random manner. The resulting face-centred tetragonal structure undergoes a disordering transformation at the critical temperature to a postulated non-quenchable face-centred cubic structure. Stresses on quenching, arising from the ordering reaction, are relieved by twinning along {101} planes or by recrystallization along with deformation twinning; always involving grain boundary fracturing.Phase relations in the system Pt-Fe-Cu have been investigated through the construction of isothermal sections at 1000 and 600°C. At 1000°C there is an extensive single phase region of solid solution around Pt2FeCu and extending to the binary composition PtFe. At 600°C the composition Pt2FeCu lies just outside this now reduced area of solid solution in a two-phase field. Comparison of the experimental results with data for tulameenite suggests that some observed compositions may be metastably preserved. The occurrence of fine veinlets of silicate or other gangue minerals in tulameenite is suggested to result from grain boundary fracturing on cooling below the critical temperature of 1178°C and to be evidence of a magmatic origin.

A Study of Cuban Todorokite

1961 ◽  
Vol 5 ◽  
pp. 117-126
Author(s):  
G. M. Faulring
Keyword(s):  
Preferred Orientation ◽  
Optical Data ◽  
X Ray Diffraction ◽  
Random Orientation ◽  
Sodium Potassium ◽  
X Ray ◽  
Cell Dimensions ◽  
Diffraction Patterns ◽  
High Degree ◽  
Manganese Oxide Mineral

AbstractTodorokite is a hydrated manganese oxide mineral containing small amounts of sodium, potassium, calcium, barium, magnesium, iron, and aluminum. From the reports of other investigators and observations in our laboratories, todorokite appears to be a more widely occurring mineral than generally recognized.It was found by X-ray diffraction that a sample of todorokite from Charco Redondo, Cuba, had a high degree of preferred orientation and that milling for a prolonged period of time was necessary to obtain random orientation in a mounted specimen. The position of the preferred orientation direction with respect to the X-ray beam is the principal factor determining the relative intensities on an X-ray diffraction pattern. Based on fiber data, the unit cell of todorokite is considered to be pseudo-orthorhombic or triclinic with α, β, and γ angles varying slightly from 90° and cell dimensions of a0 = 9.65A, b0 = 10.29A, and c0 = 2.84A, This deviation from orthogonality may account for the diffuse and distinct reflections typical of X-ray diffraction patterns of todorokite. Optical data and a hypothesized paragenesis of Cuban todorokite are also included.

scholarly journals Synthesis of the FePt nanosystem: comparison of the synthesis methods

2020 ◽  
Vol 64 (10) ◽  
pp. 33-39
Author(s):  
Nikita S. Zaharov ◽  
◽  
Anna N. Popova ◽  
Yury A. Zaharov ◽  
Olga V. Grishaeva ◽  
...  
Keyword(s):  
Hydrazine Hydrate ◽  
Sodium Tetrahydroborate ◽  
Fept Nanoparticles ◽  
Target Product ◽  
Nanosized Particles ◽  
X Ray Diffraction ◽  
Sodium Potassium ◽  
X Ray ◽  
Iron Platinum ◽  
Potassium Tartrate

In this work, using the example of the synthesis of nanoparticles of the mutual FePt system, obtained in an aqueous medium by the method of co-reduction of solutions of metal precursors, the effect of reducing agents is considered: an alkaline solution of hydrazine hydrate and sodium tetrahydroborate in combination with a stabilizer of sodium-potassium tartrate. The main characteristics of the obtained nanosized particles of the iron-platinum system were studied by means of a complex of physicochemical methods of analysis. The shape and morphology of the obtained nanosized particles were studied by transmission electron microscopy, phase analysis and X-ray structural parameters – by X-ray diffraction methods. It was approached to reveal the dependence of the particle size on the type of reducing agent used. It was found that nanosized FePt particles obtained with different reducing agents have similar physicochemical characteristics. The use of sodium tetrahydroborate, in the presence of a stabilizer sodium-potassium tartrate, allowed to obtain more dispersed particles with a size of 14.3±2.1 nm. FePt nanoparticles reduced by hydrazine hydrate were characterized by large sizes of 16.7±4.0 nm, and the particles form large dense agglomerates. Chemical analysis showed that when reducing with sodium tetrahydroborate, the target product contained 0.4 mol. % boron. When reducing FePt nanoparticles with hydrazine hydrate, it was found that the target product was contaminated with iron oxide, which was also confirmed by X-ray phase analysis. X-ray diffraction analysis showed that the iron-platinum nanosystem was represented by a solid-solution phase with a face-centred cubic lattice. The parameters of the crystal lattice were estimated, 3.908 Å and 3.894 Å, respectively, for FePt nanoparticles obtained using NaBH4 and N2H4∙H2O.

Evaluation of Freezing Methods by Low Temperature X-Ray Diffraction

1977 ◽  
Vol 35 ◽  
pp. 330-333
Author(s):  
T. Gulik-Krzywicki ◽  
M.J. Costello
Keyword(s):  
Biological Materials ◽  
Molecular Organization ◽  
X Ray Diffraction ◽  
Glass Capillary ◽  
X Ray ◽  
Rate Dependent ◽  
Before And After ◽  
Freeze Etching ◽  
Diffraction Patterns ◽  
Set Up

Freeze-etching electron microscopy is currently one of the best methods for studying molecular organization of biological materials. Its application, however, is still limited by our imprecise knowledge about the perturbations of the original organization which may occur during quenching and fracturing of the samples and during the replication of fractured surfaces. Although it is well known that the preservation of the molecular organization of biological materials is critically dependent on the rate of freezing of the samples, little information is presently available concerning the nature and the extent of freezing-rate dependent perturbations of the original organizations. In order to obtain this information, we have developed a method based on the comparison of x-ray diffraction patterns of samples before and after freezing, prior to fracturing and replication.Our experimental set-up is shown in Fig. 1. The sample to be quenched is placed on its holder which is then mounted on a small metal holder (O) fixed on a glass capillary (p), whose position is controlled by a micromanipulator.

Examination of Rabbit Fc Crystals

1968 ◽  
Vol 26 ◽  
pp. 140-141
Author(s):  
J. P. Robinson ◽  
P. G. Lenhert
Keyword(s):  
Molecular Weight ◽  
Flat Plate ◽  
Phosphate Buffer ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
Neutral Ph ◽  
Small Crystals ◽  
Carbon Coated ◽  
Diffraction Patterns

Crystallographic studies of rabbit Fc using X-ray diffraction patterns were recently reported. The unit cell constants were reported to be a = 69. 2 A°, b = 73. 1 A°, c = 60. 6 A°, B = 104° 30', space group P21, monoclinic, volume of asymmetric unit V = 148, 000 A°3. The molecular weight of the fragment was determined to be 55, 000 ± 2000 which is in agreement with earlier determinations by other methods.Fc crystals were formed in water or dilute phosphate buffer at neutral pH. The resulting crystal was a flat plate as previously described. Preparations of small crystals were negatively stained by mixing the suspension with equal volumes of 2% silicotungstate at neutral pH. A drop of the mixture was placed on a carbon coated grid and allowed to stand for a few minutes. The excess liquid was removed and the grid was immediately put in the microscope.

Control of the phase composition of advanced calcium phosphates using an x-ray diffractometer with a curved position-sensitive detector

2020 ◽  
Vol 86 (6) ◽  
pp. 29-35
Author(s):  
V. P. Sirotinkin ◽  
O. V. Baranov ◽  
A. Yu. Fedotov ◽  
S. M. Barinov
Keyword(s):  
Phase Composition ◽  
Calcium Phosphates ◽  
Position Sensitive Detector ◽  
Sensitive Detector ◽  
X Ray Diffraction ◽  
X Ray ◽  
Impurity Phases ◽  
Position Sensitive ◽  
Diffraction Peaks ◽  
Diffraction Patterns

The results of studying the phase composition of advanced calcium phosphates Ca10(PO4)6(OH)2, β-Ca3(PO4)2, α-Ca3(PO4)2, CaHPO4 · 2H2O, Ca8(HPO4)2(PO4)4 · 5H2O using an x-ray diffractometer with a curved position-sensitive detector are presented. Optimal experimental conditions (angular positions of the x-ray tube and detector, size of the slits, exposure time) were determined with allowance for possible formation of the impurity phases during synthesis. The construction features of diffractometers with a position-sensitive detector affecting the profile characteristics of x-ray diffraction peaks are considered. The composition for calibration of the diffractometer (a mixture of sodium acetate and yttrium oxide) was determined. Theoretical x-ray diffraction patterns for corresponding calcium phosphates are constructed on the basis of the literature data. These x-ray diffraction patterns were used to determine the phase composition of the advanced calcium phosphates. The features of advanced calcium phosphates, which should be taken into account during the phase analysis, are indicated. The powder of high-temperature form of tricalcium phosphate strongly adsorbs water from the environment. A strong texture is observed on the x-ray diffraction spectra of dicalcium phosphate dihydrate. A rather specific x-ray diffraction pattern of octacalcium phosphate pentahydrate revealed the only one strong peak at small angles. In all cases, significant deviations are observed for the recorded angular positions and relative intensity of the diffraction peaks. The results of the study of experimentally obtained mixtures of calcium phosphate are presented. It is shown that the graphic comparison of experimental x-ray diffraction spectra and pre-recorded spectra of the reference calcium phosphates and possible impurity phases is the most effective method. In this case, there is no need for calibration. When using this method, the total time for analysis of one sample is no more than 10 min.

Infrared spectroscopic study of the YPO4-YCrO4 system

1985 ◽  
Vol 50 (10) ◽  
pp. 2139-2145
Author(s):  
Alexander Muck ◽  
Eva Šantavá ◽  
Bohumil Hájek
Keyword(s):  
Spectroscopic Study ◽  
Infrared Spectra ◽  
Point Of View ◽  
Mixed Crystals ◽  
Crystal Symmetry ◽  
Infrared Spectroscopic Study ◽  
X Ray Diffraction ◽  
X Ray ◽  
Infrared Spectroscopic ◽  
Diffraction Patterns

The infrared spectra and powder X-ray diffraction patterns of polycrystalline YPO4-YCrO4 samples are studied from the point of view of their crystal symmetry. Mixed crystals of the D4h19 symmetry are formed over the region of 0-30 mol.% YPO4 in YCrO4. The Td → D2d → D2 or C2v(GS eff) correlation is appropriate for both PO43- and CrO43- anions.

scholarly journals Deep learning for visualization and novelty detection in large X-ray diffraction datasets

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Lars Banko ◽  
Phillip M. Maffettone ◽  
Dennis Naujoks ◽  
Daniel Olds ◽  
Alfred Ludwig
Keyword(s):  
Thin Film ◽  
Crystal Structure ◽  
Artificial Intelligence ◽  
Deep Learning ◽  
Novelty Detection ◽  
Structural Similarity ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Patterns ◽  
Post Hoc

AbstractWe apply variational autoencoders (VAE) to X-ray diffraction (XRD) data analysis on both simulated and experimental thin-film data. We show that crystal structure representations learned by a VAE reveal latent information, such as the structural similarity of textured diffraction patterns. While other artificial intelligence (AI) agents are effective at classifying XRD data into known phases, a similarly conditioned VAE is uniquely effective at knowing what it doesn’t know: it can rapidly identify data outside the distribution it was trained on, such as novel phases and mixtures. These capabilities demonstrate that a VAE is a valuable AI agent for aiding materials discovery and understanding XRD measurements both ‘on-the-fly’ and during post hoc analysis.

scholarly journals Simultaneous Multi-Bragg Peak Coherent X-ray Diffraction Imaging

Crystals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 312
Author(s):  
Florian Lauraux ◽  
Stéphane Labat ◽  
Sarah Yehya ◽  
Marie-Ingrid Richard ◽  
Steven J. Leake ◽  
...  
Keyword(s):  
Bragg Reflection ◽  
Volume Ratio ◽  
X Ray Diffraction ◽  
X Ray ◽  
Crystal Substrate ◽  
In Series ◽  
Diffraction Imaging ◽  
Diffraction Patterns ◽  
Lattice Planes ◽  
Oriented Parallel

The simultaneous measurement of two Bragg reflections by Bragg coherent X-ray diffraction is demonstrated on a twinned Au crystal, which was prepared by the solid-state dewetting of a 30 nm thin gold film on a sapphire substrate. The crystal was oriented on a goniometer so that two lattice planes fulfill the Bragg condition at the same time. The Au 111 and Au 200 Bragg peaks were measured simultaneously by scanning the energy of the incident X-ray beam and recording the diffraction patterns with two two-dimensional detectors. While the former Bragg reflection is not sensitive to the twin boundary, which is oriented parallel to the crystal–substrate interface, the latter reflection is only sensitive to one part of the crystal. The volume ratio between the two parts of the twinned crystal is about 1:9, which is also confirmed by Laue microdiffraction of the same crystal. The parallel measurement of multiple Bragg reflections is essential for future in situ and operando studies, which are so far limited to either a single Bragg reflection or several in series, to facilitate the precise monitoring of both the strain field and defects during the application of external stimuli.

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