TRY, a new computer program for crystal structure analysis from diffraction data based on internal coordinates and on a molecular modelling procedure free of redundant coordinates

2007 ◽  
Vol 40 (6) ◽  
pp. 1044-1049 ◽  
Author(s):  
Attilio Immirzi
Keyword(s):  
Computer Program ◽  
Diffraction Data ◽  
Degrees Of Freedom ◽  
Analytical Procedure ◽  
Crystal Structure Analysis ◽  
Symbolic Language ◽  
Structural Refinement ◽  
Internal Coordinates ◽  
Singular Matrices ◽  
Fibrous Polymers

A procedure is described which allows structure modelling using a number of internal coordinates that does not exceed the number of degrees of freedom of the problem. The modelling then becomes a strictly analytical procedure and structural refinement from diffraction data can be carried out avoiding the use of singular matrices. A practical `symbolic language' with a simple syntax allows easy molecular building even in intricate cases. Based on this procedure, a new computer program for the study of crystal structures (TRY), particularly suited for fibrous polymers, has been created. The program is available at http://www.theochem.unisa.it/try.html.

New solutions to the problems of chain orientation and chain continuity in structure analysis of fibrous polymers. A reconsideration of the structure of polyisobutene

2007 ◽  
Vol 40 (1) ◽  
pp. 10-15 ◽  
Author(s):  
Attilio Immirzi ◽  
Davide Alfano ◽  
Consiglia Tedesco
Keyword(s):  
New York ◽  
Degrees Of Freedom ◽  
Structure Refinement ◽  
General Interest ◽  
Structural Refinement ◽  
X Ray Diffraction ◽  
Chain Orientation ◽  
Crystalline Polymers ◽  
Internal Coordinates ◽  
Fibrous Polymers

Two points of general interest in structural refinement of polymers based on internal coordinates are discussed: the chain orientation and the chain continuity. Using a proprietary computer program, based on revised approaches to these questions, the structure of polyisobutene has been reconsidered, using new X-ray diffraction measurements (Fuji image plate) and performing a structure refinement based on internal coordinates. Three refinement schemes, with a decreasing number of degrees of freedom, have been considered, with the conclusion that the distortion from the 83regular helix, claimed by Tadokoro [(1979).Structure of Crystalline Polymers, p. 136. New York: Wiley-Interscience], is confirmed, though lower than supposed. The new procedures implemented for chain orientation and chain continuity work excellently.

scholarly journals Constraints and restraints in crystal structure analysis

2009 ◽  
Vol 42 (2) ◽  
pp. 362-364 ◽  
Author(s):  
Attilio Immirzi
Keyword(s):  
Crystal Structure ◽  
Structural Analysis ◽  
Structure Analysis ◽  
Diffraction Data ◽  
Crystal Structure Analysis ◽  
Internal Coordinates

The widely used restraint-based approach to structural analysis using diffraction data is critiqued. The convenience of using rigid constraints, through the use of internal coordinates, is discussed.

scholarly journals PSSP, a computer program for the crystal structure solution of molecular materials from X-ray powder diffraction data

2010 ◽  
Vol 43 (2) ◽  
pp. 370-376 ◽  
Author(s):  
Silvina Pagola ◽  
Peter W. Stephens
Keyword(s):  
Crystal Structure ◽  
Computer Program ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Degrees Of Freedom ◽  
Space Structure ◽  
Molecular Solids ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Structure Solution

This work describes the computer programPSSP(powder structure solution program) for the crystal structure solution of molecular solids from X-ray powder diffraction data. This direct-space structure solution program uses the simulated annealing global optimization algorithm to minimize the difference between integrated intensities calculated from trial models and those extracted in a Le Bail fit of the experimental pattern, using a cost function for dealing with peak overlap through defined intensity correlation coefficients, computationally faster to calculate thanRwp. The methodology outlined is applicable to organic solids composed of moderately complex rigid and flexible molecules, using diffraction data up to relatively low resolution.PSSPperformance tests using 11 molecular solids with six to 20 degrees of freedom are analyzed.

Structural refinement of nano BaTiO3powder using X-ray diffraction data

2004 ◽  
Vol 39 (13) ◽  
pp. 4363-4366 ◽  
Author(s):  
Yong-Il Kim ◽  
Seung-Hoon Nahm ◽  
Maeng-Joon Jung
Keyword(s):  
Diffraction Data ◽  
Structural Refinement ◽  
X Ray Diffraction ◽  
X Ray

Preparation and crystal structure of garnet-type calcium zirconium germanate Ca4ZrGe3O12

2016 ◽  
Vol 31 (4) ◽  
pp. 292-294 ◽  
Author(s):  
V. D. Zhuravlev ◽  
A. P. Tyutyunnik ◽  
N. I. Lobachevskaya
Keyword(s):  
Crystal Structure ◽  
Unit Cell Parameter ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Cell Parameter ◽  
Polycrystalline Sample ◽  
Structural Formula ◽  
Powder Diffraction Data ◽  
Structural Refinement ◽  
X Ray

A polycrystalline sample of Ca4ZrGe3O12 was synthesized using the nitrate–citrate method and heated at 850–1100 °C. Structural refinement based on X-ray powder diffraction data showed that the crystal structure is of the garnet type with a cubic unit-cell parameter [a = 12.71299(3) Å] and the space group Ia$\bar 3$d. The structural formula is presented as Ca3[CaZr]octa[Ge]tetraO12.

A program to analyze the distributions of unmeasured reflections

2011 ◽  
Vol 44 (4) ◽  
pp. 865-872 ◽  
Author(s):  
Ludmila Urzhumtseva ◽  
Alexandre Urzhumtsev
Keyword(s):  
Spatial Distribution ◽  
Missing Data ◽  
Computer Program ◽  
Diffraction Data ◽  
Reciprocal Space ◽  
Data Set ◽  
Data Completeness ◽  
Significant Time ◽  
Cumulative Data ◽  
Structure Solution

Crystallographic Fourier maps may contain barely interpretable or non-interpretable regions if these maps are calculated with an incomplete set of diffraction data. Even a small percentage of missing data may be crucial if these data are distributed non-uniformly and form connected regions of reciprocal space. Significant time and effort can be lost trying to interpret poor maps, in improving them by phase refinement or in fighting against artefacts, whilst the problem could in fact be solved by completing the data set. To characterize the distribution of missing reflections, several types of diagrams have been suggested in addition to the usual plots of completeness in resolution shells and cumulative data completeness. A computer program,FOBSCOM, has been developed to analyze the spatial distribution of unmeasured diffraction data, to search for connected regions of unmeasured reflections and to obtain numeric characteristics of these regions. By performing this analysis, the program could help to save time during structure solution for a number of projects. It can also provide information about a possible overestimation of the map quality and model-biased features when calculated values are used to replace unmeasured data.

Update in a Rietveld analysis program for x-ray powder spectro-diffractometry

2003 ◽  
Vol 18 (1) ◽  
pp. 32-35 ◽  
Author(s):  
Yanan Xiao ◽  
Fujio Izumi ◽  
Timothy Graber ◽  
P. James Viccaro ◽  
Dale E. Wittmer
Keyword(s):  
Computer Program ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Rietveld Analysis ◽  
Anomalous Scattering ◽  
Analysis Program ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Synchrotron Light ◽  
Diffraction Patterns

A computer program for refining anomalous scattering factors using x-ray powder diffraction data was revised on the basis of the latest version of a versatile pattern-fitting system, RIETAN-2000. The effectiveness of the resulting program was confirmed by applying it to simulated and measured powder-diffraction patterns of Mn3O4 taken at a synchrotron light source.

scholarly journals SUPERFLIP– a computer program for the solution of crystal structures by charge flipping in arbitrary dimensions

2007 ◽  
Vol 40 (4) ◽  
pp. 786-790 ◽  
Author(s):  
Lukáš Palatinus ◽  
Gervais Chapuis
Keyword(s):  
Computer Program ◽  
Crystal Structures ◽  
Diffraction Data ◽  
Periodic Structures ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Modulated Structures ◽  
Structure Solution ◽  
Matching Procedure ◽  
Arbitrary Dimensions

SUPERFLIPis a computer program that can solve crystal structures from diffraction data using the recently developed charge-flipping algorithm. It can solve periodic structures, incommensurately modulated structures and quasicrystals from X-ray and neutron diffraction data. Structure solution from powder diffraction data is supported by combining the charge-flipping algorithm with a histogram-matching procedure.SUPERFLIPis written in Fortran90 and is distributed as a source code and as precompiled binaries. It has been successfully compiled and tested on a variety of operating systems.

Powder X-ray diffraction of Metastudtite, (UO2)O2(H2O)2

2016 ◽  
Vol 31 (1) ◽  
pp. 71-72 ◽  
Author(s):  
Mark A. Rodriguez ◽  
Philippe E. Weck ◽  
Joshua D. Sugar ◽  
Thomas J. Kulp
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
First Principles ◽  
Density Functional ◽  
Powder Diffraction Data ◽  
Structural Refinement ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Unit Cells

There has been some confusion in the published literature concerning the structure of Metastudtite (UO2)O2(H2O)2 where differing unit cells and space groups have been cited for this compound. Owing to the absence of a refined structure for Metastudtite, Weck et al. (2012) have documented a first-principles study of Metastudtite using density functional theory (DFT). Their model presents the structure of Metastudtite as an orthorhombic (space group Pnma) structure with lattice parameters of a = 8.45, b = 8.72, and c = 6.75 Å. A Powder Diffraction File (PDF) database entry has been allocated for this hypothetical Metastudtite phase based on the DFT modeling (see 01-081-9033) and aforementioned Dalton Trans. manuscript. We have obtained phase pure powder X-ray diffraction data for Metastudtite and have confirmed the model of Weck et al. via Rietveld refinement (see Figure 1). Structural refinement of this powder diffraction dataset has yielded updated refined parameters. The new cell has been determined as a = 8.411(1), b = 8.744(1), and c = 6.505(1) Å; cell volume = 478.39 Å3. There are only subtle differences between the refined structure and that of the first-principles model derived from DFT. Notably, the b-axis is significantly contracted in the final refinement as compared with DFT. There were also subtle changes to the U1, O1, and O3 atom positions. Tabulated powder diffraction data (d's and I's) for the Metastudtite have been derived from the refined model and these new values can serve to augment the PDF entry 01-081-9033 with a more updated entry based on observed X-ray powder diffraction data.

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