scholarly journals Application of synchrotron through-the-substrate microdiffraction to crystals in polished thin sections

IUCrJ ◽  
2015 ◽  
Vol 2 (4) ◽  
pp. 452-463 ◽  
Author(s):  
Jordi Rius ◽  
Oriol Vallcorba ◽  
Carlos Frontera ◽  
Inmaculada Peral ◽  
Anna Crespi ◽  
...  

The synchrotron through-the-substrate X-ray microdiffraction technique (tts-μXRD) is extended to the structural study of microvolumes of crystals embedded in polished thin sections of compact materials [Rius, Labrador, Crespi, Frontera, Vallcorba & Melgarejo (2011).J.Synchrotron Rad.18, 891–898]. The resulting tts-μXRD procedure includes some basic steps: (i) collection of a limited number of consecutive two-dimensional patterns (frames) for each randomly oriented crystal microvolume; (ii) refinement of the metric from the one-dimensional diffraction pattern which results from circularly averaging the sum of collected frames; (iii) determination of the reciprocal lattice orientation of each randomly oriented crystal microvolume which allows assigning thehklindices to the spots and, consequently, merging the intensities of the different frames into a single-crystal data set (frame merging); and (iv) merging of the individual crystal data sets (multicrystal merging) to produce an extended data set suitable for structure refinement/solution. Its viability for crystal structure solution by Patterson function direct methods (δ recycling) and for accurate single-crystal least-squares refinements is demonstrated with some representative examples from petrology in which different glass substrate thicknesses have been employed. The section of the crystal microvolume must be at least of the same order of magnitude as the focus of the beam (15 × 15 µm in the provided examples). Thanks to its versatility and experimental simplicity, this methodology should be useful for disciplines as disparate as petrology, materials science and cultural heritage.

2013 ◽  
Vol 46 (2) ◽  
pp. 387-390 ◽  
Author(s):  
Hui Li ◽  
Xiaodong Li ◽  
Meng He ◽  
Yanchun Li ◽  
Jing Liu ◽  
...  

High-pressure single-crystal diffraction experiments often suffer from the crushing of single crystals due to the application of high pressure. Consequently, only diffraction data resulting from several particles in random orientations is available, which cannot be routinely indexed by commonly used methods designed for single-crystal data. A protocol is proposed to index such diffraction data. The techniques of powder pattern indexing are first used to propose the possible lattice parameters, and then a genetic algorithm is applied to determine the orientation of the reciprocal lattice for each of the particles. This protocol has been verified experimentally.


1995 ◽  
Vol 50 (9) ◽  
pp. 1377-1381 ◽  
Author(s):  
Olaf Reckeweg ◽  
H.-Jürgen Meyer

AbstractThe new compounds A4[Nb6Cl12(N3)6](H2O)2 (A = Rb, Cs) were synthesized from In4[Nb6Cl12Cl6] by substituting six terminal Cl ligands and the In+ ions in methanolic solution. An X-ray structure refinement was performed on single-crystal data of Rb4[Nb6Cl12(N3)6](H2O)2 (1) (space group P1̄, Z = 1, a = 912.5(1) pm, b = 937.2(1) pm, c = 1062.0(1) pm, α = 96.88(2)°, β = 101.89(1)°, γ = 101.44(2)°) and Cs4[Nb6Cl12(N3)6](H2O)2 (2) (space group PI, Z = 1, a = 920.9(5) pm, b = 947.9(7) pm, c = 1091.8(7) pm, α = 96.89(6)°, β = 103.35(5)°, γ = 101.60(5)°. Each of the centrosymmetric [Nb6Cl12(N3)6]4- ions of the isotypic compounds contains six terminal azide groups at the corners of the octahedral niobium cluster (d̄Nb-N = 226(1) pm (1), 225(1) pm (2), bond angles Nb-N-N 120-127°). The [Nb6Cl12(N3)6]4- ions are linked via Rb-N and Rb-Cl interactions of the Rb+ ions to form a three-dimensional structure. Crystals of the compounds react explosively on heating or mechanical pressure.


2007 ◽  
Vol 40 (5) ◽  
pp. 834-840 ◽  
Author(s):  
Maria Cristina Burla ◽  
Rocco Caliandro ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Liberato De Caro ◽  
...  

In the present paper, the third and last of a series (the first two papers were dedicated to the crystal structure solution of proteins), the Patterson superposition method, based on the use of the symmetry minimum function, has been applied to powder diffraction patterns. The method has been modified to take into account the special challenges of this kind of data and to optimize the performance of the approach. The new algorithms have been implemented in a computer program and applied also to single-crystal data of small and medium-size crystal structures. The experimental results have been compared with those obtainedviadirect methods, so enabling the role and the perspectives of these two approaches in the global phasing problem to be established, no matter what the experimental technique (powder or single-crystal diffraction) or the size of the structures (small, medium or macro-molecules).


1977 ◽  
Vol 31a ◽  
pp. 889-890 ◽  
Author(s):  
Rolf Berger ◽  
N. W. Larsen ◽  
H. Svanholt ◽  
Michel Pouchard ◽  
Paul Hagenmuller ◽  
...  

2013 ◽  
Vol 20 (5) ◽  
pp. 711-720 ◽  
Author(s):  
André Rothkirch ◽  
G. Diego Gatta ◽  
Mathias Meyer ◽  
Sébastien Merkel ◽  
Marco Merlini ◽  
...  

Fast detectors employed at third-generation synchrotrons have reduced collection times significantly and require the optimization of commercial as well as customized software packages for data reduction and analysis. In this paper a procedure to collect, process and analyze single-crystal data sets collected at high pressure at the Extreme Conditions beamline (P02.2) at PETRA III, DESY, is presented. A new data image format called `Esperanto' is introduced that is supported by the commercial software packageCrysAlisPro(Agilent Technologies UK Ltd). The new format acts as a vehicle to transform the most common area-detector data formatsviaa translator software. Such a conversion tool has been developed and converts tiff data collected on a Perkin Elmer detector, as well as data collected on a MAR345/555, to be imported into theCrysAlisProsoftware. In order to demonstrate the validity of the new approach, a complete structure refinement of boron-mullite (Al5BO9) collected at a pressure of 19.4 (2) GPa is presented. Details pertaining to the data collections and refinements of B-mullite are presented.


1977 ◽  
Vol 30 (9) ◽  
pp. 1929 ◽  
Author(s):  
SR Hall ◽  
CL Raston ◽  
AH White

The crystal structure of the title compound, namely hydroxyimino(N,N?- dimethyl)malonamide (MeNHCOC(=NOH)CONHMe), has been determined by single-crystal X-ray diffraction with diffractometer data at 295 K. The structure was solved by direct methods and refined by least squares to a residual of 0.055 for 1477 observed reflections. ��� Crystal data: monoclinic, P21/n, a 15.508(3), b 10.544(2), c 9.377(1) Ǻ, β 103.15(2)�, Z 8. ��� The two crystallographically independent molecules exhibit little conjugation throughout the C-C-C skeleton (<C-C> 1.50 Ǻ), the molecule being non-planar. <C=O> is 1.234, <N-CH3> 1.443, <OC-N> 1.323, <C-NO> 1.278 and (N-O) 1.375 Ǻ. The geometry is compared with those observed for several related derivatives.


2014 ◽  
Vol 70 (a1) ◽  
pp. C314-C314
Author(s):  
Gwyndaf Evans

Recent years have witnessed a marked revival of multiple crystal data collection and analysis methods. This has been brought about in many ways by a proliferation of microfocus beamlines [1] that have provided convenient access to structural biologists who wish to measure from their tiny crystals. Further to this however has been a realization that in some cases careful data collection and analysis of multiple crystal data can replace months if not years of effort in wet labs optimizing crystals to be large enough to yield a single crystal data set. The presentation will briefly discuss recent progress in multiple crystal data collection and analysis and illustrate it with some case studies.


1996 ◽  
Vol 52 (2) ◽  
pp. 328-331 ◽  
Author(s):  
S. C. Nyburg

This compound crystallizes as twins, monoclinic, space group P21/a. There being no systematic hkl absences, the chosen cell was primitive. All reciprocal lattice points hkl with h = 0 or ±3n from the twins overlap. From the non-overlapping reflections, the ratio of the masses of the two twins was obtained, but it proved impossible to partition satisfactorily the observed intensities of the overlapping reflections between the twins. Accordingly they were deleted from the data set. The remaining data did not lead to a structure solution; very small average E 2 values were obtained for all hkl reflections when (h + l) was odd, implying a (non-Bravais) B-centred monoclinic cell. The data from the larger twin were reindexed to give a primitive cell. Using direct methods, the structure was solved, showing the original cell to be B-centred, even though reflections hkl with (h + l) odd were observed. This is because these (weak) reflections all originate from the other twin. Accordingly, the reflections hkl with h = ±3n do not overlap, as had originally been supposed. These data were restored, forming a complete data set and were used to refine further the structure already obtained. The centrosymmetric dinuclear complex has a chelating dithiocarbamate ligand on each Pd atom with chloride bridges.


2020 ◽  
Author(s):  
Thu Nguyen ◽  
Kim L Phan ◽  
Dale F Kreitler ◽  
Lawrence C Andrews ◽  
Sandra B Gabelli ◽  
...  

AbstractOne often observes small but measurable differences in diffraction data measured from different crystals of a single protein. These differences might reflect structural differences in the protein and potentially reflect the natural dynamism of the molecule in solution. Partitioning these mixed-state data into single-state clusters is a critical step to extract information about the dynamic behavior of proteins from hundreds or thousands of single-crystal data sets. Mixed-state data can be obtained deliberately (through intentional perturbation) or inadvertently (while attempting to measure highly redundant single-crystal data). State changes may be expressed as changes in morphology, so that a subset of the polystates may be observed as polymorphs. After mixed-state data are deliberately or inadvertently measured, the challenge is to sort the data into clusters that may represent relevant biological polystates. Here we address this problem using a simple multi-factor clustering approach that classifies each data set using independent observables in order to assign each data set to the correct location in conformation space. We illustrate this method using two independent observables (unit cell constants and intensities) to cluster mixed-state data from chymotrypsinogen (ChTg) crystals. We observe that the data populate an arc of the reaction trajectory as ChTg is converted into chymotrypsin.


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